Diff of the two buildlogs: -- --- b1/build.log 2024-02-06 22:53:55.444072735 +0000 +++ b2/build.log 2024-02-07 05:17:07.995280293 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Feb 6 07:26:34 -12 2024 -I: pbuilder-time-stamp: 1707247594 +I: Current time: Wed Feb 7 13:03:11 +14 2024 +I: pbuilder-time-stamp: 1707260591 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -33,49 +33,81 @@ dpkg-source: info: applying extra_float_digits I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/23700/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29044/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 6 23:03 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/29044/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29044/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='0caa088b6488443f920c031d2bac3db3' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='23700' - PS1='# ' - PS2='> ' + INVOCATION_ID=1df9dfcd51844c4db8fe564b3a5e1172 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=29044 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OVWpm3NI/pbuilderrc_rQtM --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OVWpm3NI/b1 --logfile b1/build.log rdkit_202209.3-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.OVWpm3NI/pbuilderrc_RA1d --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.OVWpm3NI/b2 --logfile b2/build.log rdkit_202209.3-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff4a 6.1.0-17-armmp-lpae #1 SMP Debian 6.1.69-1 (2023-12-30) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 4964 -rwxr-xr-x 1 root root 838488 Apr 23 2023 bash @@ -135,7 +167,7 @@ -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 14152 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 133372 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 6 23:03 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 2023 su @@ -161,7 +193,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/23700/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/29044/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -602,7 +634,7 @@ Get: 330 http://deb.debian.org/debian bookworm/main armhf texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 331 http://deb.debian.org/debian bookworm/main armhf texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 332 http://deb.debian.org/debian bookworm/main armhf texlive-latex-extra all 2022.20230122-4 [19.2 MB] -Fetched 351 MB in 20s (17.8 MB/s) +Fetched 351 MB in 23s (15.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17881 files and directories currently installed.) @@ -1662,8 +1694,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Feb 6 19:30:39 UTC 2024. -Universal Time is now: Tue Feb 6 19:30:39 UTC 2024. +Local time is now: Tue Feb 6 23:12:51 UTC 2024. +Universal Time is now: Tue Feb 6 23:12:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -2016,7 +2048,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202209.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202209.3-1_source.changes +I: user script /srv/workspace/pbuilder/29044/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/29044/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202209.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202209.3-1_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202209.3-1 dpkg-buildpackage: info: source distribution unstable @@ -2158,100 +2194,92 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/rdkit-202209.3 -B/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/CMakeFiles 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.cpp -[ 2%] Linking CXX shared library ../../lib/libRDKitga.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDStreams/streams.cpp [ 3%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2022.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so @@ -2274,12 +2302,52 @@ cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2022.09.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 4%] Built target hc +[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.cpp [ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDGeneralExceptions.cpp +[ 4%] Linking CXX shared library ../../lib/libRDKitga.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2022.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2022.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 4%] Built target ga [ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.cpp [ 5%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/LocaleSwitcher.cpp +[ 5%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/versions.cpp +[ 5%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 5%] Built target RDGeneral +make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDBoost /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVect.cpp +[ 5%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp +[ 5%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.cpp In file included from /usr/include/c++/12/functional:64, from /usr/include/catch2/catch.hpp:3483, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_main.cpp:11: @@ -2292,8 +2360,6 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -[ 5%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/versions.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60: /usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]': /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 @@ -2307,28 +2373,6 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 5%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 5%] Built target RDGeneral -make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend -make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build -make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 5%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVect.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseBitVect.cpp [ 5%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so @@ -2337,32 +2381,14 @@ cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 5%] Built target EigenSolvers -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDBoost /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 5%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o -MF CMakeFiles/RDBoost.dir/Wrap.cpp.o.d -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.cpp -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/ExplicitBitVect.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/catch2/catch.hpp:566: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]', - inlined from 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)' at /usr/include/catch2/catch.hpp:12875:39: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int, const Catch::TestCase*}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 5%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testDict.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2380,51 +2406,22 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/ExplicitBitVect.cpp [ 5%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2022.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Utils.cpp cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Built target RDBoost -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend +[ 5%] Built target RDBoost +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build +make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testDict.cpp -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/base64.cpp -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitOps.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, const Catch::TestCase*}; _Tp = std::pair; _Alloc = std::allocator >]', - inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at /usr/include/catch2/catch.hpp:14244:47: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]', - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = Catch::sortTests(const IConfig&, const std::vector&)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, - inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at /usr/include/catch2/catch.hpp:14247:26: -/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1937 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1938 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1939 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = Catch::sortTests(const IConfig&, const std::vector&)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, - inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at /usr/include/catch2/catch.hpp:14247:26: -/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1854 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 5%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -2444,6 +2441,20 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/catch2/catch.hpp:566: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Catch::SectionEndInfo; _Alloc = std::allocator]', + inlined from 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)' at /usr/include/catch2/catch.hpp:12875:39: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Utils.cpp In file included from /usr/include/c++/12/vector:64: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, @@ -2463,6 +2474,10 @@ /usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1530 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int, const Catch::TestCase*}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, inlined from 'void testGithub940()' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testDict.cpp:55:16: @@ -2504,10 +2519,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteDistMat.cpp -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.cpp +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/base64.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void testVectToString()' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testDict.cpp:444:16: @@ -2520,36 +2533,183 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitOps.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue-taggedunion.h:36, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue.h:39, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:2: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void testVector() [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:71:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void testVector() [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:72:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testVector() [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:73:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator]', + inlined from 'void testVector() [with T = long double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:71:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator]', + inlined from 'void testVector() [with T = long double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:72:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testVector() [with T = long double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:73:17: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Linking CXX executable testDict cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 6%] Linking CXX static library librdkitCatch.a -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 -/usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 6%] Built target testDict -make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 6%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testConcurrentQueue.cpp +[ 6%] Linking CXX executable testRDValue +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 6%] Built target testRDValue +make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 6%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap/RDBase.cpp +[ 6%] Linking CXX executable testConcurrentQueue +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteDistMat.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 6%] Built target testConcurrentQueue +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 6%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -MF CMakeFiles/testMatrices.dir/testMatrices.cpp.o.d -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/testMatrices.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int, const Catch::TestCase*}; _Tp = std::pair; _Alloc = std::allocator >]', + inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at /usr/include/catch2/catch.hpp:14244:47: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]', + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = Catch::sortTests(const IConfig&, const std::vector&)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, + inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at /usr/include/catch2/catch.hpp:14247:26: +/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1937 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1938 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1939 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&):: >]' at /usr/include/c++/12/bits/stl_algo.h:1940:31, + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = Catch::sortTests(const IConfig&, const std::vector&)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, + inlined from 'std::vector Catch::sortTests(const IConfig&, const std::vector&)' at /usr/include/catch2/catch.hpp:14247:26: +/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1854 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap/RDBase.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/FPBReader.cpp +[ 7%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 7%] Built target testMatrices +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Catalogs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build +make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o -MF CMakeFiles/testRDValue.dir/testRDValue.cpp.o.d -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp +[ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.cpp +[ 7%] Linking CXX static library librdkitCatch.a +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 +/usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o /usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Built target rdkitCatch -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend +[ 7%] Built target rdkitCatch +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Query /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Query /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testConcurrentQueue.cpp +[ 7%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Query/CMakeFiles/testQuery.dir/test.cpp.o -MF CMakeFiles/testQuery.dir/test.cpp.o.d -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Query/test.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:25, @@ -2576,19 +2736,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Linking CXX executable testConcurrentQueue -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Built target testConcurrentQueue -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_dict.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/boost/dynamic_bitset/dynamic_bitset.hpp:27: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double&, long long unsigned int}; _Tp = std::pair; _Alloc = std::allocator >]': @@ -2643,78 +2790,39 @@ /usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1940 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o +[ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogParams.cpp +[ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/MultiFPBReader.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue-taggedunion.h:36, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDValue.h:39, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:2: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void testVector() [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:71:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void testVector() [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:72:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testVector() [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:73:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator]', - inlined from 'void testVector() [with T = long double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:71:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long double; _Alloc = std::allocator]', - inlined from 'void testVector() [with T = long double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:72:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testVector() [with T = long double]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/testRDValue.cpp:73:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_dict.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 7%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogEntry.cpp +[ 7%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2022.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 7%] Built target Catalogs +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 7%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp +[ 7%] Linking CXX executable testMatCalc +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 7%] Built target testMatCalc +make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/DistPicker.cpp In file included from /usr/include/c++/12/algorithm:61, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, @@ -2790,104 +2898,35 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Linking CXX executable dictTestsCatch -cd 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'/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Built target DataStructs -make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend -[ 6%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap 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-fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_logs.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap/RDBase.cpp -[ 6%] Linking CXX executable testRDValue -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Built target testRDValue -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testDatastructs.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap/RDBase.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 6%] Linking CXX executable logTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 7%] Linking CXX executable testQuery +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Built target logTestsCatch -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend +[ 7%] Built target testQuery +make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testFPB.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVect.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVects.h:19, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testDatastructs.cpp:17: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = ExplicitBitVect]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 6%] Linking CXX executable testFPB -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 7%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/Clustering.cpp +[ 7%] Linking CXX shared library ../../lib/libRDKitDataStructs.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2022.09.3 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Built target testFPB -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend +[ 7%] Built target DataStructs +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testMultiFPB.cpp +[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.cpp +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/MaxMinPicker.cpp In file included from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, @@ -2927,19 +2966,6 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 6%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 6%] Built target testDataStructs -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 7%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -MF CMakeFiles/cDataStructs.dir/DataStructs.cpp.o.d -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = double]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, @@ -2978,6 +3004,10 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2113 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp +[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform2D.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2985,32 +3015,45 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp:13: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/Clustering.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 7%] Linking CXX executable testMultiFPB -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 7%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 7%] Built target testMultiFPB -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend +[ 7%] Built target Clustering +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 7%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp +[ 7%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_dict.cpp +[ 8%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 8%] Built target SimDivPickers +make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 8%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_logs.cpp +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform3D.cpp In file included from /usr/include/c++/12/vector:64: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:134:28, @@ -3040,6 +3083,20 @@ /usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1530 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/catch2/catch.hpp:566, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/catch_dict.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 8%] Linking CXX executable logTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -3054,6 +3111,7 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, inlined from 'static void boost::python::vector_indexing_suite::extend(Container&, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:200:29, @@ -3064,6 +3122,10 @@ 1780 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 8%] Built target logTestsCatch +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, inlined from 'static void boost::python::vector_indexing_suite::extend(Container&, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:200:29, @@ -3074,6 +3136,9 @@ 1780 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:212:40: @@ -3100,6 +3165,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 8%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testDatastructs.cpp In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, @@ -3228,19 +3295,90 @@ 1780 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 8%] Linking CXX executable testMatrices -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/UniformGrid3D.cpp +[ 8%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 8%] Built target testMatrices -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend +[ 8%] Built target dictTestsCatch +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Catalogs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 8%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.cpp +[ 8%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testFPB.cpp +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'std::vector RDGeom::findGridTerminalPoints(const UniformGrid3D&, double, double)' at /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.cpp:163:20: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 8%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 8%] Built target RDGeometryLib +make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 8%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -MF CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o.d -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testMultiFPB.cpp +[ 8%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVect.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/BitVects.h:19, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/testDatastructs.cpp:17: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = ExplicitBitVect]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 8%] Linking CXX executable testFPB +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 8%] Built target rdBase +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -MF CMakeFiles/cDataStructs.dir/DataStructs.cpp.o.d -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 9%] Built target testFPB +make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 9%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/testTransforms.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3255,30 +3393,64 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 8%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Catalogs/CatalogParams.cpp -[ 8%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp -[ 8%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/testConrec.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3293,51 +3465,69 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 8%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 8%] Built target rdBase -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 8%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp -[ 8%] Linking CXX executable testMatCalc -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 11%] Linking CXX executable geometryTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 8%] Built target testMatCalc +[ 11%] Built target geometryTestsCatch make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 8%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o +[ 11%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp -[ 8%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /usr/include/catch2/catch.hpp:566, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/testConrec.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]', + inlined from 'void conrec::Contour(const double*, size_t, size_t, size_t, size_t, const double*, const double*, size_t, double*, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Conrec.h:196:27, + inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/testConrec.cpp:59:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 11%] Linking CXX executable testConrec +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 8%] Built target testQuery -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend +[ 11%] Built target testConrec +make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build +make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/DistPicker.cpp -[ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/MaxMinPicker.cpp +[ 11%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/testPickers.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3356,34 +3546,82 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp -[ 9%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 11%] Linking CXX executable testSimDivPickers +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 11%] Built target testSimDivPickers +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 11%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/catch_tests.cpp +[ 12%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 9%] Built target rdMetricMatrixCalc -make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend +[ 12%] Built target rdMetricMatrixCalc +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 9%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/Clustering.cpp -[ 10%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so +[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp +[ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp +[ 13%] Linking CXX executable pickersTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Built target SimDivPickers +[ 13%] Built target pickersTestsCatch make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o +[ 13%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/InfoBitRanker.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -3392,18 +3630,17 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/Clustering.cpp:12: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 10%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -3414,7 +3651,6 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = std::pair; _Sequence = std::vector >; _Compare = RDInfoTheory::gtDIPair]' at /usr/include/c++/12/bits/stl_queue.h:740:13, @@ -3428,83 +3664,32 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Built target Clustering -make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.cpp -[ 10%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so +[ 13%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Built target InfoTheory -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/testPickers.cpp -[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform2D.cpp -[ 10%] Linking CXX executable testSimDivPickers -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Built target testSimDivPickers -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build +[ 13%] Built target InfoTheory +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/catch_tests.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform3D.cpp -[ 10%] Linking CXX executable pickersTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o -o pickersTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 10%] Built target pickersTestsCatch -make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= +[ 13%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp +[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp +[ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp +[ 13%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp -[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp -[ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/UniformGrid3D.cpp +[ 13%] Built target ChemicalFeatures +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3519,7 +3704,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -3533,64 +3718,13 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'std::vector RDGeom::findGridTerminalPoints(const UniformGrid3D&, double, double)' at /build/reproducible-path/rdkit-202209.3/Code/Geometry/GridUtils.cpp:163:20: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp -[ 11%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 11%] Built target RDGeometryLib -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3598,17 +3732,35 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 13%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 13%] Built target rdGeometry +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.cpp +[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3623,14 +3775,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp -[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3638,17 +3786,16 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:11: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3663,15 +3810,27 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp -[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +In file included from /usr/include/c++/12/vector:70, + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h:29, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.cpp:12: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryAtom.cpp +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -3690,6 +3849,19 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 13%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKithc.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 13%] Built target rdSimDivPickers +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 13%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/AlignPoints.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3700,39 +3872,33 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 12%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKithc.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Built target rdSimDivPickers -make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/Data /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Data /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Data/cQuantize.cpp -[ 12%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryBond.cpp +[ 13%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2022.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Built target rdInfoTheory -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend +[ 13%] Built target Alignment +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp +[ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp +[ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3740,18 +3906,19 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp:10: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 12%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Bond.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3759,69 +3926,17 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/ML/Data/cQuantize.cpp:11: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Built target ChemicalFeatures -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.cpp -[ 12%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Built target cQuantize -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/AlignPoints.cpp -[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp -[ 12%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2022.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Built target Alignment -make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 12%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/testTransforms.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h:29, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.cpp:12: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3839,117 +3954,29 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp +[ 15%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/catch_tests.cpp -[ 15%] Linking CXX executable testGrid -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 15%] Built target testGrid -make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryBond.cpp -[ 15%] Linking CXX executable geometryTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 15%] Built target geometryTestsCatch -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend +[ 15%] Built target cDataStructs +make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ML/Data /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Data /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build +make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 15%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/testConrec.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/testConrec.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]', - inlined from 'void conrec::Contour(const double*, size_t, size_t, size_t, size_t, const double*, const double*, size_t, double*, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Conrec.h:196:27, - inlined from 'void C_A_T_C_H_T_E_S_T_0()' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/testConrec.cpp:59:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 15%] Linking CXX executable testConrec -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 15%] Built target testConrec -make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend +[ 15%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Data/cQuantize.cpp +make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.cpp -[ 16%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp +[ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/testChemicalFeatures.cpp In file included from /usr/include/c++/12/memory:66, from /usr/include/boost/iostreams/stream_buffer.hpp:15, from /usr/include/boost/iostreams/stream.hpp:21, @@ -3982,7 +4009,74 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Linking CXX executable testChemicalFeatures +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 15%] Built target testChemicalFeatures +make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 15%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/testAlignment.cpp +[ 15%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/ML/Data/cQuantize.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o ../../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 15%] Built target rdInfoTheory +make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 15%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp +[ 15%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 15%] Built target cQuantize +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -3998,10 +4092,17 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 16%] Linking CXX executable testAlignment +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 16%] Built target testAlignment +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.cpp /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindRings.cpp:1350:36: warning: unused parameter 'mol' [-Wunused-parameter] 1350 | void findRingFamilies(const ROMol &mol) { @@ -4057,6 +4158,13 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 17%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 17%] Built target rdAlignment +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RWMol.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, inlined from 'std::map > RDKit::MolOps::getMolFragsWithQuery(const RDKit::ROMol&, T (*)(const RDKit::ROMol&, const RDKit::Atom*), bool, const std::vector*, bool) [with T = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolOps.cpp:677:20: @@ -4077,8 +4185,8 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -4092,40 +4200,16 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RWMol.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 17%] Built target rdGeometry -make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 17%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp +In file included from /usr/include/c++/12/bits/stl_algobase.h:64, + from /usr/include/c++/12/bits/stl_tree.h:63, + from /usr/include/c++/12/map:60, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp:11: +/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp:96:57: required from here +/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 741 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -4134,6 +4218,12 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.h:15: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::atomicData&}; _Tp = RDKit::atomicData; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -4145,12 +4235,20 @@ 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::atomicData; _Alloc = std::allocator]', + inlined from 'RDKit::PeriodicTable::PeriodicTable()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp:47:25: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, inlined from 'unsigned int RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.cpp:426:23: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/atomic_data.cpp In file included from /usr/include/c++/12/memory:66, from /usr/include/boost/iostreams/stream_buffer.hpp:15, from /usr/include/boost/iostreams/stream.hpp:21, @@ -4180,8 +4278,6 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -4190,24 +4286,6 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -4216,6 +4294,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, @@ -4241,60 +4321,18 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, inlined from 'unsigned int RDKit::RWMol::addAtom(bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RWMol.cpp:124:23: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:64, - from /usr/include/c++/12/bits/stl_tree.h:63, - from /usr/include/c++/12/map:60, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp:11: -/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp:96:57: required from here -/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 741 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/atomic_data.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.h:15: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::atomicData&}; _Tp = RDKit::atomicData; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::atomicData; _Alloc = std::allocator]', - inlined from 'RDKit::PeriodicTable::PeriodicTable()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp:47:25: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 17%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 17%] Built target rdAlignment -make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 17%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -MF CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o.d -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/testChemicalFeatures.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp -[ 17%] Linking CXX executable testChemicalFeatures -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 17%] Built target testChemicalFeatures [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Canon.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AtomIterators.cpp /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:71:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 71 | if (res < 0) { @@ -4309,8 +4347,10 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:1081:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int, unsigned int) [with T = unsigned char; std::istream = std::basic_istream]' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:856:33: required from here /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:1666:22: warning: comparison is always false due to limited range of data type [-Wtype-limits] -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AtomIterators.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/BondIterators.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -MF CMakeFiles/GraphMol.dir/Aromaticity.cpp.o.d -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Aromaticity.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -4344,8 +4384,8 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/BondIterators.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -4354,10 +4394,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -MF CMakeFiles/GraphMol.dir/Aromaticity.cpp.o.d -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Aromaticity.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ConjugHybrid.cpp /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Kekulize.cpp: In function 'void RDKit::{anonymous}::markDbondCands(RDKit::RWMol&, const RDKit::INT_VECT&, boost::dynamic_bitset<>&, RDKit::INT_VECT&, RDKit::INT_VECT&)': @@ -4383,6 +4419,10 @@ cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Matrices.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Chirality.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RingInfo.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h:29, @@ -4404,8 +4444,8 @@ /usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 175 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RingInfo.cpp +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Renumber.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: @@ -4430,8 +4470,6 @@ /usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1530 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.cpp In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, inlined from 'void RDKit::RDProps::clearComputedProps() const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:154:25, @@ -4452,8 +4490,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Renumber.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AdjustQuery.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o @@ -4507,6 +4543,8 @@ | ^~~~~~~~~~~~~~~~~~~~ [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/new_canon.cpp +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/boost/graph/adjacency_list.hpp:16: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': @@ -4532,10 +4570,10 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FindStereo.cpp +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MonomerInfo.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:16, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.h:24, @@ -4560,6 +4598,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/NontetrahedralStereo.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::SubstanceGroup::CState}; _Tp = RDKit::SubstanceGroup::CState; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -4570,8 +4610,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MonomerInfo.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -4585,8 +4623,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/NontetrahedralStereo.cpp [ 20%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2022.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -4598,25 +4634,69 @@ make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= +make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build +make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 21%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/MolTransforms.cpp -[ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParse.cpp +[ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.cpp +[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp:103:49: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp:105:23: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 133 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp: In member function 'unsigned int RDKit::Trajectory::insertSnapshot(unsigned int, RDKit::Snapshot)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp:78:33: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 78 | return (d_snapshotVect->insert(d_snapshotVect->begin() + snapshotNum, s) - + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h:29, @@ -4631,6 +4711,20 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 21%] Built target Trajectory +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.h:14, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.cpp:10: @@ -4681,23 +4775,20 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:16: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int&, double&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int&, double&}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'RDGeom::Transform3D* MolTransforms::computeCanonicalTransform(const RDKit::Conformer&, const RDGeom::Point3D*, bool, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/MolTransforms.cpp:286:35: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 @@ -4723,98 +4814,36 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 21%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 21%] Built target GenericGroups -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp +[ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp [ 21%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 21%] Built target MolTransforms -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp:103:49: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp:105:23: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 133 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp: In member function 'unsigned int RDKit::Trajectory::insertSnapshot(unsigned int, RDKit::Snapshot)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp:78:33: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 78 | return (d_snapshotVect->insert(d_snapshotVect->begin() + snapshotNum, s) - - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 21%] Built target Trajectory -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp +[ 21%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.h:14, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp:11: @@ -4849,6 +4878,35 @@ [ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerParams.cpp In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 22%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp +[ 22%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 22%] Built target MolCatalog +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp +In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.h:32, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/SubgraphUtils.h:14, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp:11: @@ -4856,6 +4914,8 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, @@ -4870,83 +4930,39 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so +[ 22%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 21%] Built target Subgraphs -make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend +[ 22%] Built target Subgraphs +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 21%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 22%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +[ 23%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 +[ 23%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Parser.cpp /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 22%] Built target PartialCharges -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 22%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp -[ 22%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp -[ 22%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 22%] Built target rdMolTransforms -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend +[ 23%] Built target PartialCharges +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 22%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp +[ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -4956,73 +4972,27 @@ 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/smart_ptr/detail/shared_count.hpp:37, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 22%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 22%] Built target ShapeHelpers -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp -[ 23%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 23%] Built target MolCatalog -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 23%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Parser.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/algorithm/string/detail/classification.hpp:16, - from /usr/include/boost/algorithm/string/classification.hpp:18, - from /usr/include/boost/algorithm/string/trim.hpp:23, - from /usr/include/boost/algorithm/string.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.cpp:35: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:295:60, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'void RDKit::SLNParse::finalizeQueryMol(RDKit::ROMol*, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.cpp:113:17: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -5046,49 +5016,50 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&, unsigned int) [with Iterator = __gnu_cxx::__normal_iterator >]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:419:16: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&, unsigned int) [with Iterator = __gnu_cxx::__normal_iterator >]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:443:23: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, inlined from 'void RDKit::MolInterchange::{anonymous}::processMol.constprop(RDKit::RWMol*, const rapidjson::Value&, const DefaultValueCache&, const DefaultValueCache&, const RDKit::MolInterchange::JSONParseParameters&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Parser.cpp:707:52: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smarts.tab.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp [ 24%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Writer.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp In file included from /usr/include/c++/12/vector:70, - from smarts.yy:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.h:39, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.cpp:37: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/sln.tab.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Edge.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp -[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so @@ -5097,18 +5068,16 @@ cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 24%] Built target MolInterchange -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend +make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.cpp -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdqueries.cpp In file included from /usr/include/c++/12/vector:70, - from smiles.yy:12: + from sln.yy:41: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -5117,71 +5086,17 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Chirality.h:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.cpp:35: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:295:60, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'void RDKit::SLNParse::finalizeQueryMol(RDKit::ROMol*, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNParse.cpp:113:17: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp:12: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, - from smiles.ll:25: + from /usr/include/c++/12/functional:62, + from /usr/include/boost/algorithm/string/detail/classification.hpp:16, + from /usr/include/boost/algorithm/string/classification.hpp:18, + from /usr/include/boost/algorithm/string/trim.hpp:23, + from /usr/include/boost/algorithm/string.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -5190,28 +5105,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.cpp -[ 26%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 26%] Built target SmilesParse -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 26%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o -MF CMakeFiles/rdqueries.dir/rdqueries.cpp.o.d -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdqueries.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/lex.yysln.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5230,27 +5125,55 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Queries.cpp +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&, unsigned int) [with Iterator = __gnu_cxx::__normal_iterator >]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:419:16: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&, unsigned int) [with Iterator = __gnu_cxx::__normal_iterator >]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:443:23: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 24%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2022.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 24%] Built target SLNParse +make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Trajectory.cpp In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.h:39, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/SLNAttribs.cpp:37: + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Chirality.h:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Queries.cpp -[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/sln.tab.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5269,36 +5192,8 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -In file included from /usr/include/c++/12/vector:70, - from sln.yy:41: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 27%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/lex.yysln.cpp -[ 27%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 27%] Built target CIPLabeler -make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 27%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Trajectory.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smarts.tab.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5317,33 +5212,57 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 27%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2022.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -[ 27%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp:12: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +In file included from /usr/include/c++/12/vector:70, + from smarts.yy:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 25%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdTrajectory.cpp +[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smiles.tab.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 25%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 27%] Built target SLNParse +[ 25%] Built target rdqueries make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 27%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o +[ 25%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 27%] Built target rdqueries -make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 28%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5354,17 +5273,40 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdTrajectory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 28%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdTrajectory.cpp -[ 28%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 25%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 25%] Built target rdtrajectory +make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.cpp +In file included from /usr/include/c++/12/vector:70, + from smiles.yy:12: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5375,13 +5317,25 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdTrajectory.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 26%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5400,36 +5354,50 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp +[ 28%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.cpp +[ 28%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o 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../../../rdkit/Chem/rdChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 28%] Built target rdtrajectory +[ 28%] Built target rdChemicalFeatures make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.cpp -[ 28%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.cpp -[ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/LinearSearch.cpp -[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 28%] Built target rdChemicalFeatures -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend +[ 28%] Built target CIPLabeler +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build +make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -MF CMakeFiles/graphmolcpTest.dir/cptest.cpp.o.d -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/cptest.cpp +[ 28%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, + from smiles.ll:25: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5446,20 +5414,54 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 28%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +[ 28%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/LinearSearch.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 28%] Built target SmilesParse +make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 28%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ [ 28%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2022.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 28%] Built target Optimizer -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/itertest.cpp +[ 28%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:15, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructUtils.h:14, @@ -5519,490 +5521,6 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/cptest.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Linking CXX executable graphmolcpTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Built target graphmolcpTest -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/memtest1.cpp -[ 29%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Built target SubstructMatch -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test-valgrind.cpp -[ 29%] Linking CXX executable graphmolIterTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Built target graphmolIterTest -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -MF CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o.d -o CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_moliterators.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/memtest1.cpp:13: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Linking CXX executable test-valgrind -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 -[ 29%] Linking CXX executable graphmolMemTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o" -o test-valgrind ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Built target test-valgrind -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend -[ 29%] Built target graphmolMemTest1 -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Linking CXX executable moliteratorTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.dir/link.txt --verbose=1 -[ 29%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/smatest.cpp -[ 29%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/test2.cpp -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -o moliteratorTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Built target moliteratorTestsCatch -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.cpp -[ 29%] Linking CXX executable smiTest2 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Built target smiTest2 -make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Filters.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'RDKit::SparseIntVect* RDKit::getUnfoldedRDKFingerprintMol(const ROMol&, unsigned int, unsigned int, bool, bool, bool, std::vector*, const std::vector*, std::vector >*, std::map > >*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.cpp:792:40: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp -[ 29%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp -[ 29%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h:18, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp:32: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Linking CXX executable smaTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Built target smaTest1 -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 29%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o -MF CMakeFiles/testSubgraphs1.dir/test1.cpp.o.d -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/test1.cpp -[ 29%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.cpp -[ 29%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.cpp -[ 30%] Linking CXX executable testSubgraphs1 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 30%] Built target testSubgraphs1 -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 30%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/test2.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:37, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Filters.h:36, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp:32: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 30%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp -[ 30%] Linking CXX executable testSubgraphs2 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 30%] Built target testSubgraphs2 -make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make 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-[ 30%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -[ 30%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.cpp -[ 31%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp -[ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BadFileException.h:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp:13: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp -[ 32%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp -[ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h:18, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/set:60, - from /usr/include/boost/graph/adjacency_list.hpp:18: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61, - from /usr/include/boost/detail/container_fwd.hpp:94, - from /usr/include/boost/container_hash/extensions.hpp:22, - from /usr/include/boost/container_hash/hash.hpp:761, - from /usr/include/boost/functional/hash.hpp:6, - from /usr/include/boost/unordered/unordered_set.hpp:18, - from /usr/include/boost/unordered_set.hpp:17, - from /usr/include/boost/graph/adjacency_list.hpp:20: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'unsigned int RDKit::addOrder1Paths(PATH_LIST&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:54:21: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'unsigned int RDKit::addOrder1Paths(PATH_LIST&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:71:19: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:159:26: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:161:30: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:190:19: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:203:19: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:208:30: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 32%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h:18, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:33: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/set:60, - from /build/reproducible-path/rdkit-202209.3/Code/Query/SetQuery.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/Query/QueryObjects.h:29, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:23: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:19, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:28, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:25: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', - inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:123:59: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:127:64: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:128:65: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', - inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:123:59: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:127:64: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:128:65: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp -[ 32%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 32%] Built target FilterCatalog -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 32%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/test1.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.h:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.cpp -[ 33%] Linking CXX executable testPartialCharges -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 33%] Built target testPartialCharges -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 33%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdPartialCharges_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/set:60, - from /build/reproducible-path/rdkit-202209.3/Code/Query/SetQuery.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/Query/QueryObjects.h:29, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:23: -/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': -/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'OutputType RDKit::MorganFingerprint::MorganAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:153:58: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'OutputType RDKit::MorganFingerprint::MorganAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:153:58: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6017,212 +5535,39 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 33%] Built target rdPartialCharges -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/12/map:60, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:15: -/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': -/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'OutputType RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:110:58: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'OutputType RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:110:58: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/set:60, - from /usr/include/boost/graph/adjacency_list.hpp:18, - from /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h:18, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:10: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61, - from /usr/include/boost/detail/container_fwd.hpp:94, - from /usr/include/boost/container_hash/extensions.hpp:22, - from /usr/include/boost/container_hash/hash.hpp:761, - from /usr/include/boost/functional/hash.hpp:6, - from /usr/include/boost/unordered/unordered_set.hpp:18, - from /usr/include/boost/unordered_set.hpp:17, - from /usr/include/boost/graph/adjacency_list.hpp:20: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:75:17: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:83:21: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:114:17: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:141:26: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:151:30: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', - inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:167:21: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp -[ 34%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target FragCatalog -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp -[ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp -[ 34%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target rdShapeHelpers +[ 28%] Built target rdPartialCharges make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o +[ 28%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp -[ 34%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'OutputType RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:58:58: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 34%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2022.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so +[ 28%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target Fingerprints +[ 28%] Built target SubstructMatch make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -MF CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/catch_tests.cpp +[ 28%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6241,37 +5586,19 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:18, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 739 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const std::string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:239:30: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'void RDKit::MolChemicalFeatureDef::setWeights(const std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:45:21, - inlined from 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const std::string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:268:20: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 28%] Built target rdMolTransforms +make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/catch_tests.cpp:14: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': @@ -6284,35 +5611,33 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target MolChemicalFeatures -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /usr/include/c++/12/functional:62, + from /usr/include/boost/smart_ptr/detail/shared_count.hpp:37, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 28%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target rdMolCatalog +[ 28%] Built target ShapeHelpers make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o +[ 28%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp -[ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6330,50 +5655,43 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target rdCIPLabeler +[ 28%] Built target rdMolCatalog make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o +[ 28%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp -[ 34%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target ReducedGraphs +[ 28%] Built target rdCIPLabeler make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o +[ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/test.cpp -[ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6392,21 +5710,32 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 28%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../lib/libRDKitReducedGraphs.so.1 ../../../lib/libRDKitReducedGraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target rdMolInterchange +[ 28%] Built target ReducedGraphs make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o +[ 28%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -6425,75 +5754,46 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. 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-fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 34%] Built target rdSLNParse +[ 28%] Built target rdMolInterchange make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make[4]: Entering directory 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.cpp -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Edge.cpp -[ 35%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 35%] Built target testSLNParse +[ 28%] Built target rdSLNParse make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.cpp -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -cd 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CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp -[ 35%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:15, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:298:14, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'RDKit::ROMol* RDKit::Abbreviations::Utils::detail::createAbbreviationMol(const std::string&, bool, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp:181:13: +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 28%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -6518,89 +5818,84 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so +[ 28%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 35%] Built target Abbreviations +[ 28%] Built target MolAlign make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 35%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o +[ 28%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp -[ 35%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so +[ 28%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 35%] Built target MolAlign -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend +[ 28%] Built target testSLNParse +make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build +make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 35%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/testOptimizer.cpp +[ 28%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Chirality.h:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:298:14, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'RDKit::ROMol* RDKit::Abbreviations::Utils::detail::createAbbreviationMol(const std::string&, bool, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp:181:13: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/testOptimizer.cpp:14: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h:261:32: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h:285:32: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h:364:30: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 35%] Linking CXX executable testOptimizer -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 35%] Built target testOptimizer -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= +[ 29%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp +[ 29%] Built target Abbreviations +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Edge.cpp +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -6611,10 +5906,57 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'void RDKit::{anonymous}::updateSubMolConfs(const RDKit::ROMol&, RDKit::RWMol&, boost::dynamic_bitset<>&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:42:52: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void RDKit::{anonymous}::updateSubMolConfs(const RDKit::ROMol&, RDKit::RWMol&, boost::dynamic_bitset<>&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:48:28: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'RDKit::ROMol* RDKit::combineMols(const ROMol&, const ROMol&, RDGeom::Point3D)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:823:28: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp:12: + from /usr/include/c++/12/functional:62, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Chirality.h:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -6628,34 +5970,109 @@ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'void RDKit::{anonymous}::updateSubMolConfs(const RDKit::ROMol&, RDKit::RWMol&, boost::dynamic_bitset<>&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:42:52: + inlined from 'unsigned int RDKit::CoordGen::addCoords(T&, const CoordGenParams*) [with T = RDKit::ROMol]' at /build/reproducible-path/rdkit-202209.3/External/CoordGen/CoordGen.h:174:15: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void RDKit::{anonymous}::updateSubMolConfs(const RDKit::ROMol&, RDKit::RWMol&, boost::dynamic_bitset<>&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:48:28: + inlined from 'unsigned int RDKit::CoordGen::addCoords(T&, const CoordGenParams*) [with T = RDKit::ROMol]' at /build/reproducible-path/rdkit-202209.3/External/CoordGen/CoordGen.h:178:21: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'RDKit::ROMol* RDKit::combineMols(const ROMol&, const ROMol&, RDGeom::Point3D)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:823:28: + inlined from 'RDKit::ROMol* RDKit::replaceCore(const ROMol&, const ROMol&, const MatchVectType&, bool, bool, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:705:25: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 29%] Built target rdCoordGen +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 29%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/testOptimizer.cpp +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 30%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp:12: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/testOptimizer.cpp:14: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h:261:32: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h:285:32: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202209.3/Code/Numerics/Optimizer/BFGSOpt.h:364:30: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 31%] Linking CXX executable testOptimizer +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 31%] Built target testOptimizer +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make 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Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT 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/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.h:14, from /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': @@ -6668,8 +6085,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -6706,36 +6121,12 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o +[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleBend.cpp -[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'RDKit::ROMol* RDKit::replaceCore(const ROMol&, const ROMol&, const MatchVectType&, bool, bool, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:705:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 37%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp -[ 37%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +[ 32%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/BondStretch.cpp -[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/DistanceConstraint.cpp -[ 38%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so +[ 33%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 38%] Built target ChemTransforms +[ 33%] Built target ChemTransforms make -f 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'/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 38%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o +[ 33%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.cpp +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionConstraint.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/cptest.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 33%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 39%] Built target testCIPLabeler -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +[ 33%] Built target graphmolcpTest +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make 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-I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp -[ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD 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-In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.h:36, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp:32: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -[ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionConstraint.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o +[ 34%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/OopBend.cpp +[ 35%] Linking CXX executable graphmolqueryTest cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 41%] Built target graphmolqueryTest -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. 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Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/BondStretch.cpp -[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 27 | const MMFFStbn *mmffStbnParams) { | ^ -[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/OopBend.cpp -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 41%] Built target rdFingerprintGenerator -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend +[ 35%] Built target graphmolqueryTest +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +[ 35%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test-valgrind.cpp +[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionAngle.cpp In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/memtest1.cpp:13: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/TorsionAngle.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +[ 35%] Linking CXX executable graphmolMemTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 35%] Built target graphmolMemTest1 +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 35%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -MF CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o.d -o CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_moliterators.cpp +[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Nonbonded.cpp -[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o +[ 35%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd 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CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/DistanceConstraint.cpp -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 35%] Linking CXX executable test-valgrind +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now "CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o" -o test-valgrind ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 41%] Built target rdfiltercatalog -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend +[ 35%] Built target test-valgrind +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 41%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -cd 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/usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 36%] Linking CXX executable smiTest2 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 42%] Built target rdMHFPFingerprint -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend +[ 36%] Built target smiTest2 +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/test1.cpp -[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ 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CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp -[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.cpp +[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/PositionConstraint.cpp -[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o +[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 42%] Linking CXX executable testReducedGraphs -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 42%] Built target testReducedGraphs -make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend +make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build +make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 43%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp +[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Filters.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -7075,32 +6392,21 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFVdW&}; _Tp = ForceFields::MMFF::MMFFVdW; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFOop; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFOopCollection::MMFFOopCollection(bool, std::string)' at /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp:4984:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp:13: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFChg; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFChgCollection::MMFFChgCollection(std::string)' at /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp:772:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -7126,6 +6432,12 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'RDKit::SparseIntVect* RDKit::getUnfoldedRDKFingerprintMol(const ROMol&, unsigned int, unsigned int, bool, bool, bool, std::vector*, const std::vector*, std::vector >*, std::map > >*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.cpp:792:40: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFAngle; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFAngleCollection::MMFFAngleCollection(std::string)' at /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp:2149:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -7141,6 +6453,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFPBCI; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFPBCICollection::MMFFPBCICollection(std::string)' at /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp:616:25: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -7151,20 +6465,374 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 43%] Linking CXX shared library ../../lib/libRDKitForceField.so +[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp +[ 36%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2022.09.3 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 43%] Built target ForceField -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend +[ 36%] Built target ForceField +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 43%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o -MF CMakeFiles/rdchem.dir/rdchem.cpp.o.d -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdchem.cpp +[ 36%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o -MF CMakeFiles/testSubgraphs1.dir/test1.cpp.o.d -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/test1.cpp +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp +[ 36%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 36%] Built target smaTest1 +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 36%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs/test2.cpp +[ 37%] Linking CXX executable testSubgraphs1 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs1.dir/test1.cpp.o -o testSubgraphs1 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 37%] Built target testSubgraphs1 +make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h:18, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp:32: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 37%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp +[ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BadFileException.h:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp:13: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 37%] Linking CXX executable testSubgraphs2 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 37%] Built target testSubgraphs2 +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 37%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/test1.cpp +[ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp +[ 38%] Linking CXX executable testPartialCharges +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 38%] Built target testPartialCharges +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h:18, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/set:60, + from /usr/include/boost/graph/adjacency_list.hpp:18: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61, + from /usr/include/boost/detail/container_fwd.hpp:94, + from /usr/include/boost/container_hash/extensions.hpp:22, + from /usr/include/boost/container_hash/hash.hpp:761, + from /usr/include/boost/functional/hash.hpp:6, + from /usr/include/boost/unordered/unordered_set.hpp:18, + from /usr/include/boost/unordered_set.hpp:17, + from /usr/include/boost/graph/adjacency_list.hpp:20: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'unsigned int RDKit::addOrder1Paths(PATH_LIST&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:54:21: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'unsigned int RDKit::addOrder1Paths(PATH_LIST&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:71:19: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:159:26: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:161:30: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:190:19: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:203:19: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'unsigned int RDKit::addHigherOrderPaths(const INT_PATH_LIST_MAP&, const ROMol&, FragCatalog*, DOUBLE_INT_MAP&, const MatchVectType&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp:208:30: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 38%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:37, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Filters.h:36, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp:32: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp +[ 38%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.h:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 38%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp +[ 38%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.cpp +[ 39%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp +[ 40%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:18, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 739 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/set:60, + from /usr/include/boost/graph/adjacency_list.hpp:18, + from /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h:18, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:10: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = double; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp +In file included from /usr/include/c++/12/map:61, + from /usr/include/boost/detail/container_fwd.hpp:94, + from /usr/include/boost/container_hash/extensions.hpp:22, + from /usr/include/boost/container_hash/hash.hpp:761, + from /usr/include/boost/functional/hash.hpp:6, + from /usr/include/boost/unordered/unordered_set.hpp:18, + from /usr/include/boost/unordered_set.hpp:17, + from /usr/include/boost/graph/adjacency_list.hpp:20: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:75:17: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:83:21: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:114:17: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:141:26: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:151:30: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = double; _Tp = int; _Compare = RDKit::ltDouble; _Alloc = std::allocator >]', + inlined from 'void RDKit::FragFPGenerator::computeFP(const RDKit::ROMol&, const RDKit::FragCatalog&, const RDKit::MatchVectType&, ExplicitBitVect*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp:167:21: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const std::string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:239:30: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'void RDKit::MolChemicalFeatureDef::setWeights(const std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:45:21, + inlined from 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const std::string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:268:20: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 41%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 41%] Built target FragCatalog +make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 41%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp +[ 41%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 41%] Built target MolChemicalFeatures +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 41%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/test1.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7179,23 +6847,119 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202209.3/Code/Catalogs/Catalog.h:18, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:33: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/set:60, + from /build/reproducible-path/rdkit-202209.3/Code/Query/SetQuery.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/Query/QueryObjects.h:29, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:23: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:19, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:28, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:25: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', + inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:123:59: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:127:64: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:128:65: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', + inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:123:59: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:127:64: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'OutputType RDKit::AtomPair::AtomPairAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:128:65: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 41%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 43%] Built target rdReducedGraphs -make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend +[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp +[ 41%] Built target FilterCatalog +make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make 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-I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp +[ 42%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -MF CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o.d -o CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp +[ 42%] Linking CXX executable testReducedGraphs +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReducedGraphs.dir/test1.cpp.o -o testReducedGraphs ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 42%] Built target testReducedGraphs +make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o -MF CMakeFiles/rdchem.dir/rdchem.cpp.o.d -o CMakeFiles/rdchem.dir/rdchem.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdchem.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7210,10 +6974,23 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 42%] Built target rdShapeHelpers +make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 42%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7231,52 +7008,19 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 44%] Built target rdMolChemicalFeatures +[ 42%] Built target rdReducedGraphs make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 45%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o +[ 43%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -MF CMakeFiles/Depictor.dir/RDDepictor.cpp.o.d -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/RDDepictor.cpp -[ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 46%] Built target rdAbbreviations -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 46%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7291,12 +7035,44 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Table.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/12/set:60, + from /build/reproducible-path/rdkit-202209.3/Code/Query/SetQuery.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/Query/QueryObjects.h:29, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:23: +/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': +/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'OutputType RDKit::MorganFingerprint::MorganAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:153:58: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'OutputType RDKit::MorganFingerprint::MorganAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:153:58: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/SubstructMatch.h:15, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/RDDepictor.h:15, @@ -7516,13 +7292,55 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/12/map:60, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:15: +/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': +/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'OutputType RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:110:58: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'OutputType RDKit::RDKitFP::RDKitFPAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:110:58: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void RDDepict::straightenDepiction(RDKit::ROMol&, int, bool)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/RDDepictor.cpp:876:35: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o +[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp +[ 43%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 44%] Built target rdAbbreviations +[ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp +[ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Table.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7541,72 +7359,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'unsigned int RDKit::CoordGen::addCoords(T&, const CoordGenParams*) [with T = RDKit::ROMol]' at /build/reproducible-path/rdkit-202209.3/External/CoordGen/CoordGen.h:174:15: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'unsigned int RDKit::CoordGen::addCoords(T&, const CoordGenParams*) [with T = RDKit::ROMol]' at /build/reproducible-path/rdkit-202209.3/External/CoordGen/CoordGen.h:178:21: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 46%] Built target rdCoordGen -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp -In file included from /usr/include/c++/12/vector:63, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10: -/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::atomicData*]': -/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::atomicData*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::atomicData*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::atomicData*; _Tp = RDKit::atomicData]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::atomicData; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, - inlined from 'RDKit::PeriodicTable::PeriodicTable(const RDKit::PeriodicTable&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.h:32:29, - inlined from 'boost::python::objects::value_holder::value_holder(PyObject*, A0) [with A0 = boost::reference_wrapper; Value = RDKit::PeriodicTable]' at /usr/include/boost/python/object/value_holder.hpp:131:11, - inlined from 'static Holder* boost::python::objects::make_instance::construct(void*, PyObject*, boost::reference_wrapper) [with T = RDKit::PeriodicTable; Holder = boost::python::objects::value_holder]' at /usr/include/boost/python/object/make_instance.hpp:72:16, - inlined from 'static PyObject* boost::python::objects::make_instance_impl::execute(Arg&) [with Arg = const boost::reference_wrapper; T = RDKit::PeriodicTable; Holder = boost::python::objects::value_holder; Derived = boost::python::objects::make_instance >]' at /usr/include/boost/python/object/make_instance.hpp:46:31, - inlined from 'static PyObject* boost::python::objects::class_cref_wrapper::convert(const Src&) [with Src = RDKit::PeriodicTable; MakeInstance = boost::python::objects::make_instance >]' at /usr/include/boost/python/object/class_wrapper.hpp:29:37, - inlined from 'static PyObject* boost::python::converter::as_to_python_function::convert(const void*) [with T = RDKit::PeriodicTable; ToPython = boost::python::objects::class_cref_wrapper > >]' at /usr/include/boost/python/converter/as_to_python_function.hpp:40:33: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp In file included from /usr/include/c++/12/map:60, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:19, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:28, @@ -7820,24 +7572,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'RDGeom::Transform2D RDDepict::EmbeddedFrag::computeOneAtomTrans(unsigned int, const RDDepict::EmbeddedFrag&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:417:30: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -7892,6 +7626,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDDepict::EmbeddedFrag::updateNewNeighs(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:287:15: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -8117,6 +7853,21 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', + inlined from 'RDDepict::INT_PAIR_VECT RDDepict::findBondsPairsToPermuteDeg4(const RDGeom::Point2D&, const RDKit::INT_VECT&, const VECT_C_POINT&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp:382:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDDepict::EmbeddedFrag::addAtomToAtomWithAng(unsigned int, unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:646:39: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -8270,24 +8021,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDDepict::EmbeddedFrag::removeCollisionsShortenBonds()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:1803:31: /usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -8324,24 +8057,29 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', - inlined from 'RDDepict::INT_PAIR_VECT RDDepict::findBondsPairsToPermuteDeg4(const RDGeom::Point2D&, const RDKit::INT_VECT&, const VECT_C_POINT&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp:382:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp +[ 44%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2022.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 44%] Built target Depictor +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 44%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +In file included from /usr/include/c++/12/vector:63, from /usr/include/c++/12/functional:62, from /usr/include/boost/config/no_tr1/functional.hpp:21, from /usr/include/boost/function/detail/prologue.hpp:14, @@ -8352,52 +8090,78 @@ from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::atomicData*]': +/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::atomicData*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::atomicData*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::atomicData*; _Tp = RDKit::atomicData]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::atomicData; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, + inlined from 'RDKit::PeriodicTable::PeriodicTable(const RDKit::PeriodicTable&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PeriodicTable.h:32:29, + inlined from 'boost::python::objects::value_holder::value_holder(PyObject*, A0) [with A0 = boost::reference_wrapper; Value = RDKit::PeriodicTable]' at /usr/include/boost/python/object/value_holder.hpp:131:11, + inlined from 'static Holder* boost::python::objects::make_instance::construct(void*, PyObject*, boost::reference_wrapper) [with T = RDKit::PeriodicTable; Holder = boost::python::objects::value_holder]' at /usr/include/boost/python/object/make_instance.hpp:72:16, + inlined from 'static PyObject* boost::python::objects::make_instance_impl::execute(Arg&) [with Arg = const boost::reference_wrapper; T = RDKit::PeriodicTable; Holder = boost::python::objects::value_holder; Derived = boost::python::objects::make_instance >]' at /usr/include/boost/python/object/make_instance.hpp:46:31, + inlined from 'static PyObject* boost::python::objects::class_cref_wrapper::convert(const Src&) [with Src = RDKit::PeriodicTable; MakeInstance = boost::python::objects::make_instance >]' at /usr/include/boost/python/object/class_wrapper.hpp:29:37, + inlined from 'static PyObject* boost::python::converter::as_to_python_function::convert(const void*) [with T = RDKit::PeriodicTable; ToPython = boost::python::objects::class_cref_wrapper > >]' at /usr/include/boost/python/converter/as_to_python_function.hpp:40:33: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Linking CXX shared library ../../../lib/libRDKitDepictor.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2022.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'OutputType RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::getBitId(RDKit::FingerprintArguments*, const std::vector*, const std::vector*, const RDKit::AdditionalOutput*, bool, uint64_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:58:58: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 44%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2022.09.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/MHFP.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 46%] Built target Depictor -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +[ 44%] Built target Fingerprints +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Conformer.cpp -[ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.h:36, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp:32: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -8413,7 +8177,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -8424,6 +8188,23 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, @@ -8431,12 +8212,32 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Conformer.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o +[ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -8448,20 +8249,6 @@ from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10: -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 175 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -8470,29 +8257,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, - inlined from 'void RDKit::RDProps::clearComputedProps() const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:154:25, - inlined from 'void RDKit::MolClearComputedProps(const RDOb&) [with RDOb = Conformer]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/props.hpp:157:25: -/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1530 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, - inlined from 'void RDKit::RDProps::clearProp(const std::string&) const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:146:21, - inlined from 'void RDKit::MolClearProp(const RDOb&, const char*) [with RDOb = Conformer]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/props.hpp:152:16: -/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1530 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'boost::python::objects::pointer_holder::pointer_holder(PyObject*, A0) [with A0 = unsigned int; Pointer = boost::shared_ptr; Value = RDKit::Conformer]' at /usr/include/boost/python/object/pointer_holder.hpp:195:15, - inlined from 'static void boost::python::objects::make_holder<1>::apply::execute(PyObject*, t0) [with Holder = boost::python::objects::pointer_holder, RDKit::Conformer>; ArgList = boost::mpl::vector1]' at /usr/include/boost/python/object/make_holder.hpp:94:18: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp +[ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -8506,25 +8272,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8539,18 +8288,12 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp -[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:419:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); - | ^ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8565,42 +8308,16 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp -make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 48%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp -[ 48%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp -[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 46%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:419:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); + | ^ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8615,52 +8332,76 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /usr/include/c++/12/functional:62, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ForceFields::CrystalFF::ExpTorsionAngleCollection::ExpTorsionAngleCollection(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp:129:26: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 48%] Built target rdDepictor +[ 47%] Built target rdMolChemicalFeatures make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/CDXMLParser.cpp -[ 48%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 48%] Built target ForceFieldHelpers -make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/DistGeomUtils.cpp -[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/c++/12/functional:62, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8674,13 +8415,17 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp:15: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ForceFields::CrystalFF::ExpTorsionAngleCollection::ExpTorsionAngleCollection(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp:129:26: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -8699,12 +8444,37 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/TriangleSmooth.cpp +[ 47%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 47%] Built target ForceFieldHelpers +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 47%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 47%] Built target rdfiltercatalog +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 47%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(const typename _Container::value_type&) [with _Container = std::vector]' at /usr/include/c++/12/bits/stl_iterator.h:735:22, @@ -8718,8 +8488,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/DistViolationContrib.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, inlined from 'std::__detail::__unique_ptr_t<_Tp> std::make_unique(_Args&& ...) [with _Tp = RDKit::Conformer; _Args = {unsigned int}]' at /usr/include/c++/12/bits/unique_ptr.h:1065:30, @@ -8733,12 +8501,6 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp -[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/ChiralViolationContrib.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8752,27 +8514,46 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2022.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 48%] Built target DistGeometry -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend +[ 47%] Built target rdDepictor +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 49%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp +[ 47%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -8795,24 +8576,6 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::{anonymous}::ParseMol2AtomBlock(std::istream*, RDKit::RWMol*, unsigned int, RDKit::INT_VECT&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp:732:25: @@ -8831,10 +8594,6 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileParser.cpp -[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8848,28 +8607,47 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp -[ 50%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /usr/include/c++/12/functional:62, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileParser.cpp +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Built target rdForceField -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +[ 48%] Built target rdFingerprintGenerator +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/testDistGeom.cpp +[ 48%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8883,13 +8661,44 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Conformer.cpp +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 48%] Built target rdMHFPFingerprint +make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 48%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Conformer.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/numeric/conversion/converter_policies.hpp:19, @@ -8922,50 +8731,19 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Built target testDistGeom -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Built target DistGeom -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +[ 48%] Built target rdForceFieldHelpers +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/DistGeomUtils.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -8977,6 +8755,20 @@ from /usr/include/boost/python/handle.hpp:11, from /usr/include/boost/python/args_fwd.hpp:10, from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 175 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -8985,33 +8777,47 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:63: -/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]': -/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; _Tp = RDKit::Dict::Pair]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, - inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, - inlined from 'RDKit::Dict& RDKit::Dict::operator=(const RDKit::Dict&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:114:21, - inlined from 'RDKit::RDProps& RDKit::RDProps::operator=(const RDKit::RDProps&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:28:19, - inlined from 'RDKit::SubstanceGroup& RDKit::SubstanceGroup::operator=(const RDKit::SubstanceGroup&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.h:100:19: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; _Tp = RDKit::Dict::Pair]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, - inlined from 'RDKit::Dict::Dict(const RDKit::Dict&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:51:29, - inlined from 'RDKit::RDProps::RDProps(const RDKit::RDProps&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:23:33, - inlined from 'RDKit::SubstanceGroup::SubstanceGroup(const RDKit::SubstanceGroup&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.h:99:3: -/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, + inlined from 'void RDKit::RDProps::clearComputedProps() const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:154:25, + inlined from 'void RDKit::MolClearComputedProps(const RDOb&) [with RDOb = Conformer]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/props.hpp:157:25: +/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1530 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, + inlined from 'void RDKit::RDProps::clearProp(const std::string&) const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:146:21, + inlined from 'void RDKit::MolClearProp(const RDOb&, const char*) [with RDOb = Conformer]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/props.hpp:152:16: +/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1530 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'boost::python::objects::pointer_holder::pointer_holder(PyObject*, A0) [with A0 = unsigned int; Pointer = boost::shared_ptr; Value = RDKit::Conformer]' at /usr/include/boost/python/object/pointer_holder.hpp:195:15, + inlined from 'static void boost::python::objects::make_holder<1>::apply::execute(PyObject*, t0) [with Holder = boost::python::objects::pointer_holder, RDKit::Conformer>; ArgList = boost::mpl::vector1]' at /usr/include/boost/python/object/make_holder.hpp:94:18: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp +[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/TriangleSmooth.cpp +[ 48%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 48%] Built target O3AAlign +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 49%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp +[ 49%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/DistViolationContrib.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9026,14 +8832,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp -[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -9048,23 +8850,48 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp +[ 49%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/ChiralViolationContrib.cpp +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp +[ 50%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2022.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Built target rdForceFieldHelpers -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend +[ 50%] Built target DistGeometry +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp +[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -9083,41 +8910,181 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 50%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::vector RDKit::SGroupParsing::ParseV3000Array(std::stringstream&, int, bool) [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp:957:21: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp +[ 50%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Built target rdchem -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend +[ 50%] Built target rdForceField +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp -[ 50%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +[ 50%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/testDistGeom.cpp +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp +[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 50%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.so.1.2022.09.3 ../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 50%] Built target testDistGeom +make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 50%] Built target O3AAlign +make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 50%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp -[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::DGeomHelpers::detail::embedHelper_(int, int, EmbedArgs*, const RDKit::DGeomHelpers::EmbedParameters*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:1037:27: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 50%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 50%] Built target DistGeom +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'void RDKit::DGeomHelpers::EmbedMultipleConfs(RDKit::ROMol&, RDKit::INT_VECT&, unsigned int, const EmbedParameters&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:1118:55: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp:15: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileWriter.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp +[ 51%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 51%] Built target DistGeomHelpers +[ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /usr/include/boost/iterator/iterator_concepts.hpp:26, @@ -9140,14 +9107,6 @@ /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]': /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, @@ -9157,19 +9116,8 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::DGeomHelpers::detail::embedHelper_(int, int, EmbedArgs*, const RDKit::DGeomHelpers::EmbedParameters*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:1037:27: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'void RDKit::DGeomHelpers::EmbedMultipleConfs(RDKit::ROMol&, RDKit::INT_VECT&, unsigned int, const EmbedParameters&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:1118:55: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1908 | __introsort_loop(_RandomAccessIterator __first, @@ -9178,19 +9126,64 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BadFileException.h:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = Rankers::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'unsigned int RDKit::{anonymous}::getAtomParityFlag(const RDKit::Atom*, const RDKit::Conformer*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileWriter.cpp:513:12, @@ -9213,30 +9206,12 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SDWriter.cpp -[ 51%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BadFileException.h:16, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:11: @@ -9244,15 +9219,12 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 51%] Built target DistGeomHelpers In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', inlined from 'unsigned int RDKit::SDMolSupplier::length()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:261:29: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', inlined from 'virtual RDKit::ROMol* RDKit::SDMolSupplier::next()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:168:23: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 @@ -9271,8 +9243,67 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/BadFileException.h:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /usr/include/c++/12/functional:62, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SmilesWriter.cpp +In file included from /usr/include/c++/12/vector:63: +/usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]': +/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; _Tp = RDKit::Dict::Pair]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1617:35, + inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/vector.tcc:232:44, + inlined from 'RDKit::Dict& RDKit::Dict::operator=(const RDKit::Dict&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:114:21, + inlined from 'RDKit::RDProps& RDKit::RDProps::operator=(const RDKit::RDProps&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:28:19, + inlined from 'RDKit::SubstanceGroup& RDKit::SubstanceGroup::operator=(const RDKit::SubstanceGroup&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.h:100:19: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]' at /usr/include/c++/12/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; _Tp = RDKit::Dict::Pair]' at /usr/include/c++/12/bits/stl_uninitialized.h:372:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:601:31, + inlined from 'RDKit::Dict::Dict(const RDKit::Dict&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:51:29, + inlined from 'RDKit::RDProps::RDProps(const RDKit::RDProps&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:23:33, + inlined from 'RDKit::SubstanceGroup::SubstanceGroup(const RDKit::SubstanceGroup&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstanceGroup.h:99:3: +/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp In file included from /usr/include/c++/12/vector:70, @@ -9304,6 +9335,11 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TDTWriter.cpp +[ 52%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 52%] Built target rdchem [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileParser.cpp In file included from /usr/include/c++/12/vector:70, @@ -9315,6 +9351,8 @@ /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileWriter.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: @@ -9354,8 +9392,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileWriter.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBParser.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/numeric/conversion/converter_policies.hpp:19, @@ -9375,6 +9413,8 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBWriter.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -9388,10 +9428,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBParser.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBWriter.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PDBSupplier.cpp In file included from /usr/include/c++/12/vector:70, @@ -9491,18 +9527,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.cpp:13: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SVGParser.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, @@ -9520,12 +9546,24 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SVGParser.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.cpp:13: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/PNGParser.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -9540,6 +9578,8 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::{anonymous}::ptreeToMol(RDKit::RWMol*, const boost::property_tree::ptree&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SVGParser.cpp:46:20, @@ -9561,10 +9601,6 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h:29, @@ -9610,28 +9646,44 @@ make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/CoordGen /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 55%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/CoordGen/test.cpp [ 55%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/testUFFForceField.cpp +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test1.cpp [ 55%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/testMMFFForceField.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/testUFFForceField.cpp:14: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, from /build/reproducible-path/rdkit-202209.3/External/CoordGen/test.cpp:13: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': @@ -9649,18 +9701,19 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/testUFFForceField.cpp:14: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test1.cpp:12: +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 175 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: @@ -9686,6 +9739,21 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -9701,19 +9769,6 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 55%] Built target testCoordGen -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test1.cpp -[ 55%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 55%] Built target testUFFForceField make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= @@ -9722,20 +9777,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/molopstest.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/test1.cpp:12: -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 175 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 55%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 55%] Linking CXX executable testUFFForceField +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 55%] Built target testMMFFForceField +[ 55%] Built target testUFFForceField make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= @@ -9744,21 +9790,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testChirality.cpp -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -9792,6 +9823,19 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp +[ 56%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 56%] Built target testMMFFForceField +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -9816,11 +9860,50 @@ from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp:33: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp:60:14: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp:61:14: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp:62:14: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.h:15, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 523 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 56%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, @@ -9828,6 +9911,16 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 56%] Built target graphmoltestPicklerGlobalSetting +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 56%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/hanoitest.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, inlined from 'void testGithubIssue2510()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1499:31: @@ -9853,6 +9946,75 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'void testGithub2441()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1424:31: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'void testGithub2441()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1428:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1071:14: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1072:14: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1073:14: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 57%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 57%] Built target graphmoltestChirality +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 57%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/resMolSupplierTest.cpp +[ 57%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 57%] Built target hanoiTest +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 57%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testMolBundle.cpp +[ 57%] Linking CXX executable graphmoltestPickler +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 57%] Built target graphmoltestPickler +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 57%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testSGroup.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/bits/random.h:34, from /usr/include/c++/12/random:49, @@ -9887,20 +10049,12 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 57%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, inlined from 'void testGithubIssue678()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/molopstest.cpp:6273:33: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 57%] Built target graphmoltestChirality -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, inlined from 'void testIssue212()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/molopstest.cpp:1975:31: @@ -9914,11 +10068,6 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -9937,139 +10086,11 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'void testGithub2441()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1424:31: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'void testGithub2441()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1428:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1071:14: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1072:14: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPickler.cpp:1073:14: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp:33: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp:60:14: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp:61:14: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp:62:14: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 57%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 57%] Built target graphmoltestPickler -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 57%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/hanoitest.cpp -[ 57%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 57%] Built target graphmoltestPicklerGlobalSetting -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 57%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/resMolSupplierTest.cpp [ 58%] Linking CXX executable resMolSupplierTest cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 58%] Built target resMolSupplierTest -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 58%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testMolBundle.cpp -[ 58%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 58%] Built target hanoiTest -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 58%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/testSGroup.cpp -[ 58%] Linking CXX executable molBundleTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 58%] Built target molBundleTest make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake --color= @@ -10078,11 +10099,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 58%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_graphmol.cpp -[ 58%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 58%] Linking CXX executable molBundleTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 58%] Built target graphmolMolOpsTest +[ 58%] Built target molBundleTest make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= @@ -10102,6 +10123,16 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/catch2/catch.hpp:566, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_sgroups.cpp:12: @@ -10113,32 +10144,35 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Linking CXX executable graphmolSGroupCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -In file included from /usr/include/c++/12/vector:70, - from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_graphmol.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 58%] Linking CXX executable testSGroup +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 58%] Built target graphmolSGroupCatch +[ 58%] Built target testSGroup make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 58%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_adjustquery.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/catch2/catch.hpp:566, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_graphmol.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_adjustquery.cpp +[ 58%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -10147,11 +10181,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Linking CXX executable testSGroup -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 58%] Built target testSGroup +[ 58%] Built target graphmolSGroupCatch make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake --color= @@ -10167,6 +10198,19 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 59%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 59%] Built target graphmolMolOpsTest +make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 59%] Building CXX object Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_canon.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, @@ -10179,16 +10223,6 @@ [ 59%] Linking CXX executable graphmolAdjustQueryCatch cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 59%] Built target graphmolAdjustQueryCatch -make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 59%] Building CXX object Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_canon.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, inlined from 'void C_A_T_C_H_T_E_S_T_35()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_graphmol.cpp:260:34: @@ -10202,6 +10236,16 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 59%] Built target graphmolAdjustQueryCatch +make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 60%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/testDepictor.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/catch2/catch.hpp:566, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_canon.cpp:11: @@ -10215,24 +10259,11 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 59%] Linking CXX executable graphmolTestsCatch +[ 60%] Linking CXX executable graphmolTestsCatch cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 59%] Built target graphmolTestsCatch -make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 60%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/testDepictor.cpp -[ 60%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 60%] Built target canonTestsCatch +[ 60%] Built target graphmolTestsCatch make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake --color= @@ -10241,11 +10272,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/catch_tests.cpp -[ 60%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 60%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 60%] Built target depictorCatch +[ 60%] Built target canonTestsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= @@ -10659,11 +10690,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/cxsmiles_test.cpp -[ 60%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 60%] Linking CXX executable depictorCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 60%] Built target chiralityTestsCatch +[ 60%] Built target depictorCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake --color= @@ -10685,16 +10716,33 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 60%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp +[ 60%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 60%] Built target chiralityTestsCatch +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/test1.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/catch_tests.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/catch_tests.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -10703,23 +10751,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] Linking CXX executable nontetrahedralCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 60%] Built target nontetrahedralCatch -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/test1.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -10735,24 +10766,24 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 61%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 60%] Linking CXX executable nontetrahedralCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 61%] Built target smiTest1 +[ 60%] Built target nontetrahedralCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o +[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMolSupplier.cpp -[ 62%] Linking CXX executable smiTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 62%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 62%] Built target smiTestCatch +[ 62%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake --color= @@ -10786,9 +10817,32 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Linking CXX executable testGeneralFileReader +[ 62%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 62%] Built target smiTestCatch +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp +[ 63%] Linking CXX executable testGeneralFileReader cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 63%] Built target testGeneralFileReader +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMolWriter.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/test1.cpp:11: @@ -10802,21 +10856,11 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 62%] Built target testGeneralFileReader -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, @@ -10877,27 +10921,14 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 63%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 /usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 63%] Linking CXX executable testMolSupplier -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 63%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -[ 63%] Built target testMolSupplier -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMolWriter.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 63%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' @@ -10907,32 +10938,19 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testTpls.cpp -[ 64%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 63%] Linking CXX executable testMolSupplier +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Built target fileParsersTest1 +[ 63%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 64%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Built target testTplParser -make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testSequence.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -10950,32 +10968,32 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 64%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 63%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Built target testSequence -make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend +[ 63%] Built target testTplParser +make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -[ 64%] Linking CXX executable testMol2ToMol +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testSequence.cpp +[ 63%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Built target testMol2ToMol -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend +[ 63%] Built target testMol2ToMol +make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, @@ -11004,11 +11022,24 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 64%] Linking CXX executable testMolWriter +[ 63%] Linking CXX executable testMolWriter cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Built target testMolWriter +[ 63%] Built target testMolWriter +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp +[ 64%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 64%] Built target fileParsersTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= @@ -11017,11 +11048,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testPropertyLists.cpp -[ 64%] Linking CXX executable testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 64%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Built target testExtendedStereoParsing +[ 64%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake --color= @@ -11030,29 +11061,19 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 64%] Linking CXX executable testExtendedStereoParsing +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 64%] Built target testExtendedStereoParsing +make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/catch2/catch.hpp:566, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/testPropertyLists.cpp:11: @@ -11069,19 +11090,6 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 64%] Built target XYZFileParserCatchTest -make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp -[ 64%] Linking CXX executable testPropertyLists -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 64%] Built target testPropertyLists make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= @@ -11090,28 +11098,35 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 64%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/test1.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/catch2/catch.hpp:566, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'void C_A_T_C_H_T_E_S_T_65()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp:1565:33: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void C_A_T_C_H_T_E_S_T_65()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp:1567:21: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'void C_A_T_C_H_T_E_S_T_59()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp:1366:35: + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 64%] Linking CXX executable cdxmlParserCatchTest cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 64%] Linking CXX executable testPropertyLists +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 64%] Built target cdxmlParserCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend @@ -11122,11 +11137,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct/catch_tests.cpp -[ 65%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 65%] Built target fileParsersCatchTest +[ 65%] Built target testPropertyLists make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake --color= @@ -11136,6 +11148,19 @@ [ 65%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -MF CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o.d -o CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/generic_tests.cpp In file included from /usr/include/c++/12/vector:70, + from /usr/include/catch2/catch.hpp:566, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/generic_tests.cpp:13: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, @@ -11153,14 +11178,30 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so [ 65%] Linking CXX executable substructTestCatch cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'void C_A_T_C_H_T_E_S_T_65()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp:1565:33: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void C_A_T_C_H_T_E_S_T_65()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp:1567:21: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 65%] Built target testSubstructMatch +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'void C_A_T_C_H_T_E_S_T_59()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp:1366:35: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 65%] Built target substructTestCatch make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= @@ -11169,8 +11210,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o -MF CMakeFiles/Descriptors.dir/Crippen.cpp.o.d -o CMakeFiles/Descriptors.dir/Crippen.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Crippen.cpp +[ 65%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 65%] Built target substructTestCatch +[ 65%] Built target testSubstructMatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= @@ -11179,19 +11223,19 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups/generic_tests.cpp:13: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 65%] Linking CXX executable testGenericGroups +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 65%] Built target testGenericGroups +make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 65%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/catch_tests.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -11214,21 +11258,43 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 65%] Linking CXX executable testGenericGroups -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 65%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 65%] Built target testGenericGroups -make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend +[ 65%] Built target fileParsersCatchTest +make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build +make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 65%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/catch_tests.cpp +[ 65%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/catch2/catch.hpp:566, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/catch_tests.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp:68:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 68 | const std::vector &atom_props) { + | ^ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp:32: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/alloc_traits.h:33, from /usr/include/c++/12/ext/alloc_traits.h:34, from /usr/include/c++/12/bits/basic_string.h:39, @@ -11270,46 +11336,12 @@ /usr/include/c++/12/bits/new_allocator.h:137:55: note: at offset [8, 56] into destination object of size 56 allocated by 'operator new' 137 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp:68:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 68 | const std::vector &atom_props) { - | ^ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms/catch_tests.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 65%] Built target testChemTransforms -make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 65%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -MF CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o.d -o CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp [ 65%] Linking CXX executable chemTransformsTestCatch cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so @@ -11323,6 +11355,31 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 66%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/test1.cpp +[ 66%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 66%] Built target filterCatalogTest +make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.h:14, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp:11: @@ -11330,6 +11387,9 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 66%] Linking CXX executable testChemTransforms +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::pair RDKit::Descriptors::BCUT2D(const RDKit::ROMol&, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp:98:20: @@ -11348,39 +11408,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolDescriptors.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp:32: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Linking CXX executable filterCatalogTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 66%] Built target filterCatalogTest -make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -[ 66%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 66%] Built target testFragCatalog +[ 66%] Built target testChemTransforms make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= @@ -11389,8 +11418,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/test1.cpp -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11409,8 +11436,23 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o +[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolDescriptors.cpp +[ 66%] Linking CXX executable testFragCatalog +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 66%] Built target testFragCatalog +make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11429,21 +11471,21 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Lipinski.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -MF CMakeFiles/Descriptors.dir/MolSurf.cpp.o.d -o CMakeFiles/Descriptors.dir/MolSurf.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.cpp +[ 67%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 67%] Built target testMHFPFingerprint +make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -11477,10 +11519,23 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Lipinski.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11516,20 +11571,8 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MQN.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11548,36 +11591,84 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/set:60, + from /build/reproducible-path/rdkit-202209.3/Code/Query/SetQuery.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/Query/QueryObjects.h:29, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:12: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:19, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:28, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:25: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::SparseIntVect::setVal(IndexType, int) [with IndexType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:95:13, + inlined from 'void testRDKitFP()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:1461:20: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ [ 67%] Linking CXX executable testFingerprints cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::SparseIntVect::setVal(IndexType, int) [with IndexType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:95:13, + inlined from 'void testTopologicalTorsionFPOld()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:1593:20: +/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 512 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 513 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MQN.cpp [ 67%] Built target testFingerprints -make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend +make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build +make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp +[ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp [ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp -[ 67%] Linking CXX executable testMHFPFingerprint -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 67%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 67%] Built target testMHFPFingerprint -make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend +[ 67%] Built target testFingerprintGenerators +make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build +make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp +[ 67%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -11596,49 +11687,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.h:36, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp:32: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'std::vector RDKit::Descriptors::Properties::computeProperties(const RDKit::ROMol&, bool) const' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp:170:18: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR2D.cpp -[ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 67%] Built target rdfragcatalog -make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp In file included from /usr/include/c++/12/vector:64, from /usr/include/catch2/catch.hpp:566, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:11: @@ -11677,6 +11725,110 @@ | ^ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:666:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:666:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 +[ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 67%] Built target rdfragcatalog +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:36:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:47:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:58:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:59:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:68:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:69:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:83:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:84:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:98:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:99:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:100:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_29()': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:537:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 537 | } @@ -11706,8 +11858,16 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:537:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:537:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:537:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/USRDescriptor.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void testWeightedCentroid()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:400:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_23()': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:402:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 402 | } @@ -11721,6 +11881,37 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:402:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:402:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:402:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 +[ 67%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 67%] Built target testMolTransforms +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.h:36, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp:32: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_17()': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:275:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 275 | } @@ -11740,40 +11931,12 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:275:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:275:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/catch_tests.cpp:275:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 -In file included from /usr/include/c++/12/set:60, - from /build/reproducible-path/rdkit-202209.3/Code/Query/SetQuery.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/Query/QueryObjects.h:29, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:12: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:19, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:28, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Atom.h:25: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::SparseIntVect::setVal(IndexType, int) [with IndexType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:95:13, - inlined from 'void testRDKitFP()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:1461:20: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::SparseIntVect::setVal(IndexType, int) [with IndexType = long long unsigned int]' at /build/reproducible-path/rdkit-202209.3/Code/DataStructs/SparseIntVect.h:95:13, - inlined from 'void testTopologicalTorsionFPOld()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp:1593:20: -/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 512 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 513 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'std::vector RDKit::Descriptors::Properties::computeProperties(const RDKit::ROMol&, bool) const' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp:170:18: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/catch2/catch.hpp: In function 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = std::_Rb_tree_const_iterator > > >; Sentinel = std::_Rb_tree_const_iterator > > >]': /usr/include/catch2/catch.hpp:1829:21: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator > > >' changed in GCC 7.1 1829 | std::string rangeToString(InputIterator first, Sentinel last) { @@ -11831,150 +11994,38 @@ /usr/include/catch2/catch.hpp:2019:77: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator > > >' changed in GCC 7.1 2019 | return ::Catch::Detail::rangeToString( begin( range ), end( range ) ); | ^ -[ 68%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 68%] Built target testFingerprintGenerators -make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp -[ 68%] Linking CXX executable fpTestCatch +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR2D.cpp +[ 67%] Linking CXX executable fpTestCatch cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 68%] Built target fpTestCatch -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend +[ 67%] Built target fpTestCatch +make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build +make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AtomFeat.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:36:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:47:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:58:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:59:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:68:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:69:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:83:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:84:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:98:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:99:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:100:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void testWeightedCentroid()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/test1.cpp:400:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/EEM.cpp -[ 68%] Linking CXX executable testMolTransforms -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 67%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp +[ 68%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 68%] Built target testMolTransforms -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend +[ 68%] Built target testMMFFForceFieldHelpersMultiThread +make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build +make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp +[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -11994,72 +12045,16 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 68%] Built target testMMFFForceFieldHelpers -make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/EEM.cpp:31: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 69%] Built target testMMFFForceFieldHelpersMultiThread -make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 69%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp:51: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'double RDKit::Descriptors::PBF(const RDKit::ROMol&, int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp:129:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.cpp -[ 69%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 69%] Built target testCrystalForceField make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 69%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o +[ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp +[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/USRDescriptor.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -12074,24 +12069,11 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 69%] Linking CXX executable testCrystalForceField +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 69%] Built target testUFFForceFieldHelpers +[ 69%] Built target testCrystalForceField make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake --color= @@ -12100,8 +12082,21 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 69%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR3D.cpp +[ 69%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 69%] Built target testUFFForceFieldHelpers +make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 69%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp +[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AtomFeat.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/catch2/catch.hpp:566, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp:11: @@ -12129,23 +12124,26 @@ /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/EEM.cpp In file included from /usr/include/c++/12/map:61, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:19, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:28, @@ -12168,97 +12166,34 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable distGeomHelpersCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:34: -/usr/include/c++/12/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 739 | vector<_Tp, _Alloc>:: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 69%] Linking CXX executable distGeomHelpersCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [ 69%] Built target distGeomHelpersCatch -make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:115:12, - inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, - inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:116:12, - inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, - inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:117:12, - inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, - inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:118:12, - inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, - inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:119:12, - inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, - inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:120:12, - inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, - inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build +make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 69%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp +[ 69%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/catch_tests.cpp In file included from /usr/include/c++/12/set:60, from /build/reproducible-path/rdkit-202209.3/Code/Query/SetQuery.h:13, from /build/reproducible-path/rdkit-202209.3/Code/Query/QueryObjects.h:29, @@ -12281,8 +12216,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MORSE.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void testGithub2246()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:2216:17: /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -12442,6 +12375,435 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:60, + from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, + from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, + from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:5: +/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/map:61: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'RDKit::INT_VECT RDKit::EmbedMultipleConfs(ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool, bool, bool, unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:88:12: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'int RDKit::EmbedMolecule(ROMol&, unsigned int, int, bool, bool, double, bool, unsigned int, boost::python::dict&, double, bool, bool, bool, bool, bool, bool, bool, unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:39:12: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 69%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 69%] Built target rdDistGeom +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 69%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/EEM.cpp:31: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 70%] Linking CXX executable testDistGeomHelpers +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Built target testDistGeomHelpers +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp +[ 70%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Built target molAlignCatchTest +make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/test1.cpp +[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:14: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp:51: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'double RDKit::Descriptors::PBF(const RDKit::ROMol&, int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp:129:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 70%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Built target testShapeHelpers +make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test6()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:417:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test6()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:418:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test6()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:419:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:890:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:891:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:892:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:896:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:897:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:898:19: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 70%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Built target testMolCatalog +make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.cpp +In file included from /usr/include/boost/bind.hpp:30, + from /usr/include/boost/property_tree/json_parser/detail/parser.hpp:7, + from /usr/include/boost/property_tree/json_parser/detail/read.hpp:13, + from /usr/include/boost/property_tree/json_parser.hpp:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.cpp:16: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 70%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Built target testFeatures +make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/trajectoryTest.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR3D.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 70%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2022.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libz.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Built target MMPA +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/test1.cpp +[ 71%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Seed.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/trajectoryTest.cpp:13: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 72%] Linking CXX executable trajectoryTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so 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Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 72%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/molinterchange_catch.cpp +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/test1.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp +[ 72%] Linking CXX executable molInterchangeCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 72%] Built target molInterchangeCatchTest +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolfiles.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:34: +/usr/include/c++/12/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 739 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:115:12, + inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, + inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:116:12, + inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, + inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:117:12, + inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, + inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:118:12, + inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, + inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:119:12, + inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, + inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:120:12, + inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:151:13, + inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp:211:11: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/MORSE.cpp +[ 72%] Linking CXX executable molInterchangeTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 72%] Built target molInterchangeTest1 +make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 72%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/catch_tests.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolfiles.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -12520,111 +12882,62 @@ 1780 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 70%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Built target testDistGeomHelpers -make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/catch_tests.cpp -[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp: In function 'Eigen::MatrixXd RDKit::Descriptors::{anonymous}::GetPinv(const Eigen::MatrixXd&)': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp:282:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'Eigen::Index' {aka 'int'} [-Wsign-compare] 282 | for (unsigned int i = 0; i < A.cols(); ++i) { | ~~^~~~~~~~~~ -[ 70%] Linking CXX executable molAlignCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp +[ 72%] Linking CXX executable testAbbreviations +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Built target molAlignCatchTest -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend +[ 72%] Built target testAbbreviations +make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build +make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp -In file included from /usr/include/c++/12/map:60, - from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, - from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, - from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:5: -/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/map:61: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'RDKit::INT_VECT RDKit::EmbedMultipleConfs(ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool, bool, bool, unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:88:12: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int RDKit::EmbedMolecule(ROMol&, unsigned int, int, bool, bool, double, bool, unsigned int, boost::python::dict&, double, bool, bool, bool, bool, bool, bool, bool, unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:39:12: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 72%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +In file included from /usr/include/c++/12/vector:70, + from /usr/include/c++/12/functional:62, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 72%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2022.09.3 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libz.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Built target rdDistGeom -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend +[ 72%] Built target FMCS +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build +make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:14: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 72%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp In file included from /usr/include/c++/12/bits/stl_algo.h:60, from /usr/include/c++/12/algorithm:61, from /usr/include/boost/iterator/iterator_concepts.hpp:26, @@ -12651,69 +12964,19 @@ 1802 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test6()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:417:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test6()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:418:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test6()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:419:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:890:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:891:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:892:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:896:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:897:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void testGithub2077()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp:898:19: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 72%] Linking CXX executable testMMPA +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 72%] Built target testMMPA +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 72%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': @@ -12766,71 +13029,79 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Built target testShapeHelpers -make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/test1.cpp -[ 70%] Linking CXX executable testFeatures -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Built target testFeatures -make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void RDKit::Descriptors::{anonymous}::getGETAWAYDescCustom(Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, int, std::vector, const RDKit::ROMol&, std::vector&, unsigned int, const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp:387:25: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/bind.hpp:30, - from /usr/include/boost/property_tree/json_parser/detail/parser.hpp:7, - from /usr/include/boost/property_tree/json_parser/detail/read.hpp:13, - from /usr/include/boost/property_tree/json_parser.hpp:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/FMCS.cpp:16: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void RDKit::Descriptors::{anonymous}::getGETAWAYDesc(Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, int, std::vector, const RDKit::ROMol&, std::vector&, unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp:610:25: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Built target testMolCatalog -make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend +[ 72%] Built target rdMMPA +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 70%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.cpp -[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o +[ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp +[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/WHIM.cpp -[ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Seed.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp:34: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -12839,51 +13110,78 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 72%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2022.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libz.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 72%] Built target MMPA -make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 72%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/trajectoryTest.cpp -[ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory/trajectoryTest.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp:46: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 73%] Linking CXX executable trajectoryTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 74%] Linking CXX executable testFMCS +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Built target trajectoryTest -make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend +[ 74%] Built target testFMCS +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/test1.cpp +[ 74%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp +[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/test1.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -12892,40 +13190,100 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/CoulombMat.cpp -[ 73%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp +[ 74%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2022.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /usr/include/c++/12/functional:62, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::setStreamIndices(SDMolSupplier&, boost::python::api::object)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp:35:18: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Built target molInterchangeTest1 -make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend +[ 74%] Built target Descriptors +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -[ 73%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2022.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so +[ 74%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 74%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Built target Descriptors -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend +[ 74%] Built target rdFMCS +make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build +make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolfiles.cpp -[ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp -[ 73%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 74%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/hashfunctions.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -12940,40 +13298,98 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolfiles.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::string testChEMBL_Txt(const char*, double, const char*)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:550:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 550 | fprintf(fres, "%s;%lu;%.1f;%.4f;%u;%u;%s;", test, mols.size(), th, sec, + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1232:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1232 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1244:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1244 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1350:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1350 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1403:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1403 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1492:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] + 1492 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), + | ~~^ ~~~~~~~~~~~ + | | | + | long unsigned int std::vector >::size_type {aka unsigned int} + | %u +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'RDKit::ROMOL_SPTR RDKit::RCore::replaceCoreAtomsWithMolMatches(bool&, const RDKit::ROMol&, const RDKit::MatchVectType&) const' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp:124:57: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/../../RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:47: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:295:60, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'void test504()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:498:18: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp +[ 74%] Linking CXX executable FMCStest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Built target molInterchangeCatchTest -make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/catch_tests.cpp -[ 73%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2022.09.3 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libz.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Built target FMCS +[ 74%] Built target FMCStest make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o +[ 74%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.cpp +[ 75%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/normalize.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.cpp:35: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -12982,32 +13398,103 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 73%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/MDLParser.cpp -[ 73%] Linking CXX executable testAbbreviations -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/normalize.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 75%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2022.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Built target testAbbreviations +[ 75%] Built target MolHash make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/test.cpp In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.cpp:35: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/MDLParser.cpp +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp:11: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/DaylightParser.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupData.h:13, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupMatch.h:12, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp:11: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -13018,12 +13505,8 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/DaylightParser.cpp -[ 74%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionPickler.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 77%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/algorithm/string/detail/classification.hpp:16, @@ -13049,12 +13532,16 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +[ 77%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 78%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp In file included from /usr/include/c++/12/vector:64: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void testProperties()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/test.cpp:1892:20: @@ -13073,42 +13560,23 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp -[ 74%] Linking CXX executable testDescriptors +[ 78%] Linking CXX executable testDescriptors cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDescriptors.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDescriptors.dir/test.cpp.o -o testDescriptors ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 74%] Built target testDescriptors +[ 78%] Built target testDescriptors make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o +[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp:35: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:295:60, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'void {anonymous}::setRXNRoleOfAllMoleculeAtoms(RDKit::ROMol&, int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp:51:19: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp +[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13123,114 +13591,98 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionDepict.cpp -[ 74%] Linking CXX executable testAUTOCORR2D +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp:17: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::GaResult}; _Tp = RDKit::GaResult; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::GaResult&}; _Tp = RDKit::GaResult; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +[ 78%] Linking CXX executable testAUTOCORR2D cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 74%] Built target testAUTOCORR2D +[ 78%] Built target testAUTOCORR2D make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o +[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testATF.cpp -[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp -[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp -[ 75%] Linking CXX executable testATF -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::GaResult}; _Tp = RDKit::GaResult; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::GaResult; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector]' at /usr/include/c++/12/bits/stl_iterator.h:743:22, + inlined from '_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator*, vector > >; _OIter = back_insert_iterator >; _UnaryOperation = RDKit::RGroupGa::runBatch()::&)>]' at /usr/include/c++/12/bits/stl_algo.h:4263:12, + inlined from 'std::vector RDKit::RGroupGa::runBatch()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp:332:19: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::GaResult; _Alloc = std::allocator]', + inlined from 'std::vector RDKit::RGroupGa::runBatch()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp:338:24: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp:35: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:295:60, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'void {anonymous}::setRXNRoleOfAllMoleculeAtoms(RDKit::ROMol&, int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp:51:19: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 79%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitga.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 75%] Built target testATF +[ 79%] Built target RGroupDecomposition make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o +[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o -MF CMakeFiles/testBCUT.dir/testBCUT.cpp.o.d -o CMakeFiles/testBCUT.dir/testBCUT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testBCUT.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionUtils.cpp -[ 75%] Linking CXX executable testBCUT -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionDepict.cpp +[ 79%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp +[ 79%] Linking CXX executable testATF +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 75%] Built target testBCUT +[ 79%] Built target testATF make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o +[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testEEM.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::setStreamIndices(SDMolSupplier&, boost::python::api::object)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDMolSupplier.cpp:35:18: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionUtils.cpp:33: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp -[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/MoleculeParser.cpp +[ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionFingerprints.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13245,27 +13697,40 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 75%] Linking CXX executable testEEM -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEEM.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEEM.dir/testEEM.cpp.o -o testEEM ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 79%] Linking CXX executable testBCUT +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testBCUT.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testBCUT.dir/testBCUT.cpp.o -o testBCUT ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 75%] Built target testEEM +[ 79%] Built target testBCUT make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f 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-I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/testPBF.cpp.o -MF CMakeFiles/testPBF.dir/testPBF.cpp.o.d -o CMakeFiles/testPBF.dir/testPBF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testPBF.cpp -[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 79%] Built target testEEM +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -MF CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o.d -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testRDFcustom.cpp +[ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o +cd 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -13281,19 +13746,17 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Linking CXX executable testPBF +[ 79%] Linking CXX executable testPBF cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPBF.dir/testPBF.cpp.o -o testPBF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 75%] Built target testPBF -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend +[ 79%] Built target testPBF +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -MF CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o.d -o CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testRDFcustom.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13308,27 +13771,18 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o -MF CMakeFiles/testRDF.dir/testRDF.cpp.o.d -o CMakeFiles/testRDF.dir/testRDF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testRDF.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp:35: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::ReactionRunnerUtils::generateProductConformers(RDKit::Conformer*, const RDKit::ROMol&, ReactantProductAtomMapping*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp:1286:30: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionUtils.cpp:33: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -13349,73 +13803,38 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp -[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && 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-MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -[ 76%] Linking CXX executable testRDFcustom +[ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/MoleculeParser.cpp +[ 80%] Linking CXX executable testRDFcustom cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 76%] Built target testRDFcustom -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend +[ 80%] Built target testRDFcustom +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 76%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/testRDF.cpp.o -MF CMakeFiles/testRDF.dir/testRDF.cpp.o.d -o CMakeFiles/testRDF.dir/testRDF.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testRDF.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 77%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp -[ 77%] Linking CXX executable testRDF +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testMORSE.cpp +[ 80%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +[ 80%] Linking CXX executable testRDF cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 77%] Built target testRDF -make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend +[ 80%] Built target testRDF +make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testMORSE.cpp -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.h:36, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp:32: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -MF CMakeFiles/test3D.dir/test3D.cpp.o.d -o CMakeFiles/test3D.dir/test3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/test3D.cpp +[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13430,29 +13849,17 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/PNGParser.cpp -[ 78%] Linking CXX executable testMORSE +[ 80%] Linking CXX executable testMORSE cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMORSE.dir/testMORSE.cpp.o -o testMORSE ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Built target testMORSE -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -MF CMakeFiles/test3D.dir/test3D.cpp.o.d -o CMakeFiles/test3D.dir/test3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/test3D.cpp -[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/CDXMLParser.cpp -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp +[ 80%] Built target testMORSE +[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/algorithm/string/detail/classification.hpp:16, @@ -13470,24 +13877,9 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 80%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, @@ -13530,36 +13922,131 @@ /usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1032 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 78%] Linking CXX executable test3D -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Built target test3D +[ 80%] Built target rdmolfiles make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testWHIM.dir/testWHIM.cpp.o -MF CMakeFiles/testWHIM.dir/testWHIM.cpp.o.d -o CMakeFiles/testWHIM.dir/testWHIM.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testWHIM.cpp -[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp -[ 78%] Linking CXX executable testWHIM -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp:35: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::ReactionRunnerUtils::generateProductConformers(RDKit::Conformer*, const RDKit::ROMol&, ReactantProductAtomMapping*)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp:1286:30: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 80%] Linking CXX executable test3D +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Built target testWHIM +[ 80%] Built target test3D make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o +[ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/PNGParser.cpp +[ 81%] Linking CXX executable testWHIM +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so 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Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 81%] Built target testGETAWAY +make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -MF CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o.d -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testCoulombMat.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.h:39, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.h:36, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp:32: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/CDXMLParser.cpp +[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp +[ 81%] Linking CXX executable testAUTOCORR3D +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 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/usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 81%] Built target testAUTOCORR3D +make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/catch_tests.cpp +[ 82%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 82%] Built target testCoulombMat +make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDescriptors_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -MF CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o.d -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13567,17 +14054,33 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp:11: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:436:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 436 | python::list atomprops) { + | ^ +[ 82%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 82%] Built target descriptorsTestCatch +make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 82%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testMolAlign.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/numeric/conversion/converter_policies.hpp:19, @@ -13603,23 +14106,75 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp -[ 78%] Linking CXX executable testGETAWAY -cd 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/usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp +[ 82%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -MF CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o.d -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp -[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK 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CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 82%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp +In file included from /usr/include/c++/12/bits/stl_algobase.h:64, + from /usr/include/c++/12/string:50, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Matrix.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/SquareMatrix.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform3D.h:16, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: +/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here +/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 741 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:14: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::pair {anonymous}::{anonymous}::BCUT2D_tuple(const RDKit::ROMol&, boost::python::tuple)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:448:19: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:439:19: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 82%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 82%] Built target ChemReactions +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 82%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/catch_tests.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13634,27 +14189,48 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:14: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp -[ 78%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp -[ 78%] Linking CXX executable testAUTOCORR3D -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'RDKit::MolAlign::PyO3A* RDKit::MolAlign::getCrippenO3A(RDKit::ROMol&, RDKit::ROMol&, boost::python::list, boost::python::list, int, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:431:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 431 | (python::len(prbCrippenContribs) == prbNAtoms)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:446:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 446 | (python::len(refCrippenContribs) == refNAtoms)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'boost::python::tuple RDKit::MolAlign::getCrippenO3AForConfs(RDKit::ROMol&, RDKit::ROMol&, int, boost::python::list, boost::python::list, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:507:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 507 | (python::len(prbCrippenContribs) == prbNAtoms)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:522:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] + 522 | (python::len(refCrippenContribs) == refNAtoms)) { + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 82%] Linking CXX executable testO3AAlign +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Built target testAUTOCORR3D -make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend +[ 82%] Built target testO3AAlign +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -MF CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o.d -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/testCoulombMat.cpp +[ 82%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13669,50 +14245,90 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp:13: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 78%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 78%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 82%] Linking CXX executable molHashCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 78%] Built target testCoulombMat -make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend +[ 82%] Built target molHashCatchTest +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect 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-I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.cpp +[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so 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'/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Built target ChemReactions -make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend +[ 82%] Built target rdMolDescriptors +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap 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-I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -MF CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o.d -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp -[ 79%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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-I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp +[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Built target rdmolfiles -make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend +[ 83%] Built target rdMolHash +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testMolAlign.cpp +[ 83%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp +[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 83%] Built target rdMolAlign +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 83%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.cpp:11: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 83%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2022.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 83%] Built target Deprotect +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 83%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13720,59 +14336,99 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:10: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:34: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:436:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 436 | python::list atomprops) { - | ^ -[ 79%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp:32: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 83%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Built target descriptorsTestCatch -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend +[ 83%] Built target rgroupCatchTests +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp -[ 79%] Linking CXX executable testMolAlign -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolops.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp:32: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolops.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 83%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Built target testMolAlign -make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend +[ 83%] Built target testRGroupDecompInternals +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -In file included from /usr/include/c++/12/bits/stl_algobase.h:64, - from /usr/include/c++/12/string:50, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Matrix.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/SquareMatrix.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/Transform3D.h:16, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: -/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here -/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 741 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ +[ 83%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp +[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitga.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolOps.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 83%] Built target rdRGroupDecomposition +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -13787,67 +14443,576 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:14: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolOps.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:14: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::pair {anonymous}::{anonymous}::BCUT2D_tuple(const RDKit::ROMol&, boost::python::tuple)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:448:19: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:439:19: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 83%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/PositionVariation.cpp +[ 83%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 83%] Built target testRGroupDecomp +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp +[ 84%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/LinkNode.cpp +[ 84%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 84%] Built target testReactionFingerprints +make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp:34: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'RDKit::EnumerationTypes::RGROUPS RDKit::getSizesFromBBs(const std::vector >&) [with T = boost::shared_ptr]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:79:20, + inlined from 'void RDKit::EnumerationStrategyBase::initialize(const RDKit::ChemicalReaction&, const RDKit::EnumerationTypes::BBS&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:149:41: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'RDKit::MolAlign::PyO3A* RDKit::MolAlign::getCrippenO3A(RDKit::ROMol&, RDKit::ROMol&, boost::python::list, boost::python::list, int, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:431:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 431 | (python::len(prbCrippenContribs) == prbNAtoms)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:446:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 446 | (python::len(refCrippenContribs) == refNAtoms)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'boost::python::tuple RDKit::MolAlign::getCrippenO3AForConfs(RDKit::ROMol&, RDKit::ROMol&, int, boost::python::list, boost::python::list, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:507:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 507 | (python::len(prbCrippenContribs) == prbNAtoms)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:522:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] - 522 | (python::len(refCrippenContribs) == refNAtoms)) { - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 79%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 84%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +[ 84%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 84%] Built target testEnumeration +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp +[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp +In file included from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:10: +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_72()': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1257:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1257 | CHECK(mol->getProp("CDX_REAGENT_ID") == i++); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1264:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1264 | CHECK(mol->getProp("CDX_PRODUCT_ID") == i++); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 85%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 85%] Built target MolEnumerator +make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 85%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 85%] Built target rdmolops +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:25, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.h:20, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:33: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 523 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2541:27: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2542:21: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2543:21: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2544:21: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, + inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2551:27: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2552:21: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, + inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2553:21: +/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1032 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /usr/include/c++/12/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8: +/usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': +/usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, + | ^~~~~~~~~ +/usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/12/vector:70, + from /usr/include/c++/12/functional:62, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:14, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10: +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 189 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 175 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 739 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', + inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, + inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, + inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:279:49: +/usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2112 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2113 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', + inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, + inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, + inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:286:53, + inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:273:9: +/usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2112 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2113 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', + inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, + inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, + inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:279:49: +/usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2112 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2113 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', + inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, + inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, + inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:286:53, + inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:273:9: +/usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2112 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2113 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Metal.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Linking CXX executable rxnTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Built target testO3AAlign +[ 85%] Built target rxnTestCatch make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o +[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp +In file included from /usr/include/c++/12/vector:64: +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:134:28, + inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:128:9, + inlined from 'static void boost::python::detail::slice_helper::base_delete_slice(Container&, PySliceObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:697:42, + inlined from 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:256:49: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::delete_item(Container&, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:124:28, + inlined from 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:263:41: +/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1530 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:134:28, + inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:128:9, + inlined from 'static void boost::python::detail::slice_helper::base_delete_slice(Container&, PySliceObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:697:42, + inlined from 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:256:49: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::delete_item(Container&, index_type) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:124:28, + inlined from 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:263:41: +/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1530 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void boost::python::container_utils::extend_container(Container&, boost::python::api::object) [with Container = std::vector]' at /usr/include/boost/python/suite/indexing/container_utils.hpp:36:36: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void boost::python::container_utils::extend_container(Container&, boost::python::api::object) [with Container = std::vector]' at /usr/include/boost/python/suite/indexing/container_utils.hpp:44:40: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'static void boost::python::vector_indexing_suite::extend(Container&, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:200:29, + inlined from 'static void boost::python::vector_indexing_suite::base_extend(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:236:36: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'static void boost::python::vector_indexing_suite::extend(Container&, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:200:29, + inlined from 'static void boost::python::vector_indexing_suite::base_extend(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:236:36: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, + inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:212:40: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, + inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:220:44, + inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:206:9: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, + inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:212:40: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, + inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:220:44, + inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:206:9: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:639:43: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:103:33, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:639:43: +/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:648:47: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:103:33, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:648:47: +/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:664:43: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:672:47: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:113:33, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:116:32, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:117:33, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:639:43: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:103:33, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:639:43: +/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:648:47: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:103:33, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:648:47: +/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:664:43: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:672:47: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:113:33, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:116:32, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: +/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, + inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:117:33, + inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 1779 | _M_range_insert(__pos, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ + 1780 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Normalize.cpp In file included from /usr/include/c++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/string:50, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:17, @@ -13859,19 +15024,8 @@ /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 79%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Built target rdMolAlign -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp +[ 85%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22: @@ -14060,19 +15214,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 79%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 85%] Linking CXX executable testReaction +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Built target rdMolDescriptors -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend +[ 85%] Built target testReaction +make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build +make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 79%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp +[ 85%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/deprotectTest.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/12/bits/stl_map.h:858:27, inlined from 'void RDKit::MolDraw2D::makeReactionComponents(const std::vector >&, const std::vector*, int, std::map&, std::vector >&, double&, double&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:871:36: @@ -14089,8 +15243,68 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 639 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:34: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Validate.cpp +[ 87%] Linking CXX executable deprotectTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 87%] Built target deprotectTest +make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 88%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 88%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp +[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:16: +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 175 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Charge.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -14105,13 +15319,30 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp:46: +In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', + inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: +/usr/include/boost/smart_ptr/shared_ptr.hpp:416:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] + 416 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) + | ~~^~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here + 129 | ROMOL_SPTR react = python::extract(reactant); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: +In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', + inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:416:72, + inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: +/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] + 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) + | ~~^~~ +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here + 129 | ROMOL_SPTR react = python::extract(reactant); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -14120,68 +15351,21 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp -[ 81%] Linking CXX executable testFMCS -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 81%] Built target testFMCS -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 81%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::string testChEMBL_Txt(const char*, double, const char*)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:550:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 550 | fprintf(fres, "%s;%lu;%.1f;%.4f;%u;%u;%s;", test, mols.size(), th, sec, - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet_SMI(const char*, const char*)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1232:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1232 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s;", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1244:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1244 | fprintf(fcsv, "%u;%lu;%s;%.3f;%u;%u;%s\n", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'void testFileSDF_RandomSet(const char*, const char*)': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1350:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1350 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1403:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1403 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:1492:29: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] - 1492 | fprintf(fcsv, "%u;%lu;%s;%.5f;%u;%u;%s;", n, mols.size(), - | ~~^ ~~~~~~~~~~~ - | | | - | long unsigned int std::vector >::size_type {aka unsigned int} - | %u -[ 81%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 81%] Built target rdFMCS -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= +In file included from /usr/include/c++/12/vector:64: +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, + inlined from 'void RDKit::RDProps::clearComputedProps() const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:154:25, + inlined from 'void RDKit::MolClearComputedProps(const RDOb&) [with RDOb = ChemicalReaction]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/props.hpp:157:25: +/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1530 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, + inlined from 'void RDKit::RDProps::clearProp(const std::string&) const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:146:21, + inlined from 'void RDKit::MolClearProp(const RDOb&, const char*) [with RDOb = ChemicalReaction]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/props.hpp:152:16: +/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1530 | { return _M_erase(begin() + (__position - cbegin())); } + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp:11: @@ -14189,11 +15373,6 @@ /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 81%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/hashfunctions.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]', inlined from 'void RDKit::MolDraw2D_detail::arcPoints(const RDGeom::Point2D&, const RDGeom::Point2D&, std::vector&, float, float)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp:46:21: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -14228,15 +15407,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/../../RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:47: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -14247,30 +15417,21 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:286:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:295:60, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'void test504()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:498:18: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o +[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp -[ 81%] Linking CXX executable FMCStest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +[ 88%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 81%] Built target FMCStest -make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend +[ 88%] Built target rdDeprotect +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf 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Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 81%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +[ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -14286,8 +15447,21 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 82%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 89%] Built target rdChemReactions +make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 89%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:28: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]': @@ -14299,56 +15473,12 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] Linking CXX executable testMMPA -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -o testMMPA ../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 82%] Built target testMMPA -make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMMPA_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -MF CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o.d -o CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp In file included from /usr/include/c++/12/map:60, from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:17: /usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/normalize.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] Linking CXX shared library ../../../lib/libRDKitMolHash.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2022.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 82%] Built target MolHash -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -14362,32 +15492,18 @@ from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 82%] Built target rdMMPA -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.cpp:11: + from /usr/include/c++/12/functional:62, + from /usr/include/boost/function.hpp:23, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -14396,76 +15512,54 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp -[ 82%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2022.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Fragment.cpp +[ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 82%] Built target Deprotect -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= +[ 89%] Built target rdMolEnumerator +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +[ 89%] Linking CXX executable testMolEnumerator +cd 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../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolops.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdmolops.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o +[ 89%] Built target testMolEnumerator +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.cpp -[ 82%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolOps.cpp +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp:34: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp:10: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/MolOps.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp In file included from /usr/include/c++/12/algorithm:61, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.cpp:13: /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, std::vector&)::&, const pair&)> >]': @@ -14495,6 +15589,24 @@ /usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/12/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter >]': /usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1782 | __unguarded_linear_insert(_RandomAccessIterator __last, @@ -14532,6 +15644,8 @@ /usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -14563,6 +15677,8 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.cpp:338:43: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 338 | std::vector points{p1, p2}; | ^ +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -14660,8 +15776,16 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = RDKit::MolDraw2D_detail::DrawMol::makeBondHighlightLines(double, double)::]' at /usr/include/c++/12/bits/stl_algo.h:4853:18, inlined from 'void RDKit::MolDraw2D_detail::DrawMol::makeBondHighlightLines(double, double)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.cpp:2128:20: @@ -14702,32 +15826,14 @@ /usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1854 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -[ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp In file included from /usr/include/c++/12/vector:64, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ROMol.h:29, @@ -14771,40 +15877,20 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawShape.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 83%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'RDKit::ROMOL_SPTR RDKit::RCore::replaceCoreAtomsWithMolMatches(bool&, const RDKit::ROMol&, const RDKit::MatchVectType&) const' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp:124:57: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 83%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawText.cpp In file included from /usr/include/c++/12/vector:64, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawShape.cpp:15: @@ -14823,6 +15909,22 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawShape.h:29:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 29 | const DashPattern shortDashes{2.0, 2.0}; | ^ +In file included from /usr/include/c++/12/vector:70, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h:14, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70: /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -15057,26 +16159,8 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawText.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp In file included from /usr/include/c++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/string:50, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawText.h:19, @@ -15086,91 +16170,52 @@ /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 83%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp -[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so 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/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +[ 91%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 84%] Built target rdmolops -make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend +[ 91%] Built target MolStandardize +make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make 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-I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp -[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp -[ 84%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 84%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/PositionVariation.cpp -[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o +[ 91%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/TautomerQuery.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp -[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextJS.cpp -[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupData.h:13, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupMatch.h:12, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp:11: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 84%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/LinkNode.cpp -[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp -[ 85%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp -[ 85%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ 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CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp +[ 92%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 92%] Built target TautomerQuery +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/test1.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:28, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp:17: @@ -15184,142 +16229,167 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp:17: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::GaResult}; _Tp = RDKit::GaResult; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::GaResult&}; _Tp = RDKit::GaResult; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::GaResult}; _Tp = RDKit::GaResult; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::GaResult; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(typename _Container::value_type&&) [with _Container = std::vector]' at /usr/include/c++/12/bits/stl_iterator.h:743:22, - inlined from '_OIter std::transform(_IIter, _IIter, _OIter, _UnaryOperation) [with _IIter = __gnu_cxx::__normal_iterator*, vector > >; _OIter = back_insert_iterator >; _UnaryOperation = RDKit::RGroupGa::runBatch()::&)>]' at /usr/include/c++/12/bits/stl_algo.h:4263:12, - inlined from 'std::vector RDKit::RGroupGa::runBatch()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp:332:19: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::GaResult; _Alloc = std::allocator]', - inlined from 'std::vector RDKit::RGroupGa::runBatch()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp:338:24: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 85%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitga.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 85%] Built target RGroupDecomposition -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 85%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp -[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp -[ 86%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 86%] Built target MolEnumerator -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testNormalize.cpp +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp -[ 87%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so +[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testValidate.cpp +[ 93%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libcairo.so cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Built target MolDraw2D -make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend +[ 93%] Built target MolDraw2D +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp -[ 87%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so 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-DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testCharge.cpp +[ 93%] Linking CXX executable molNormalizeTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 93%] Linking CXX executable molValidateTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Built target testReactionFingerprints -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +[ 93%] Built target molNormalizeTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testTautomer.cpp +[ 94%] Built target molValidateTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize 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/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 95%] Built target molFragmentTest +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 96%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/utils.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp:34: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /usr/include/catch2/catch.hpp:566, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/catch_tests.cpp:10: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'RDKit::EnumerationTypes::RGROUPS RDKit::getSizesFromBBs(const std::vector >&) [with T = boost::shared_ptr]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:79:20, - inlined from 'void RDKit::EnumerationStrategyBase::initialize(const RDKit::ChemicalReaction&, const RDKit::EnumerationTypes::BBS&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:149:41: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:10: -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_72()': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1257:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1257 | CHECK(mol->getProp("CDX_REAGENT_ID") == i++); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1264:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 1264 | CHECK(mol->getProp("CDX_PRODUCT_ID") == i++); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -[ 87%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp +[ 96%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Built target testEnumeration -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend +[ 96%] Built target ScaffoldNetwork +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp +[ 96%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 96%] Built target molStandardizeCatchTest +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -MF CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o.d -o CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp +[ 96%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/catch_tests.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -15327,328 +16397,29 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /usr/include/c++/12/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8: -/usr/include/c++/12/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': -/usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2059 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, - | ^~~~~~~~~ -/usr/include/c++/12/bits/stl_algobase.h:2059:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:14, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10: -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator, iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 189 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc:189:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 175 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 739 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/12/bits/vector.tcc:739:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', - inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, - inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, - inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:279:49: -/usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2112 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2113 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', - inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, - inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, - inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:286:53, - inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:273:9: -/usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2112 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2113 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', - inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, - inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, - inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:279:49: -/usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2112 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2113 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', - inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/12/bits/stl_algo.h:3851:28, - inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, - inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:286:53, - inlined from 'static bool boost::python::indexing_suite::base_contains(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:273:9: -/usr/include/c++/12/bits/stl_algobase.h:2112:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2112 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2113 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:134:28, - inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:128:9, - inlined from 'static void boost::python::detail::slice_helper::base_delete_slice(Container&, PySliceObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:697:42, - inlined from 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:256:49: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::delete_item(Container&, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:124:28, - inlined from 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; bool NoProxy = true; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:263:41: -/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1530 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:134:28, - inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:128:9, - inlined from 'static void boost::python::detail::slice_helper::base_delete_slice(Container&, PySliceObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:697:42, - inlined from 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:256:49: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::delete_item(Container&, index_type) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:124:28, - inlined from 'static void boost::python::indexing_suite::base_delete_item(Container&, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; bool NoProxy = false; bool NoSlice = false; Data = long long unsigned int; Index = unsigned int; Key = long long unsigned int]' at /usr/include/boost/python/suite/indexing/indexing_suite.hpp:263:41: -/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1530 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void boost::python::container_utils::extend_container(Container&, boost::python::api::object) [with Container = std::vector]' at /usr/include/boost/python/suite/indexing/container_utils.hpp:36:36: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void boost::python::container_utils::extend_container(Container&, boost::python::api::object) [with Container = std::vector]' at /usr/include/boost/python/suite/indexing/container_utils.hpp:44:40: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'static void boost::python::vector_indexing_suite::extend(Container&, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:200:29, - inlined from 'static void boost::python::vector_indexing_suite::base_extend(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:236:36: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'static void boost::python::vector_indexing_suite::extend(Container&, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:200:29, - inlined from 'static void boost::python::vector_indexing_suite::base_extend(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:236:36: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, - inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:212:40: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, - inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:220:44, - inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:206:9: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, - inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:212:40: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::append(Container&, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:193:32, - inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:220:44, - inlined from 'static void boost::python::vector_indexing_suite::base_append(Container&, boost::python::api::object) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:206:9: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:639:43: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:103:33, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:639:43: -/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:648:47: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:103:33, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:648:47: -/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:664:43: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:672:47: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:113:33, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:116:32, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:117:33, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, false>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, false> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:639:43: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:103:33, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:639:43: -/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:102:32, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:648:47: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:103:33, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, const data_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:95:9, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:648:47: -/usr/include/c++/12/bits/vector.tcc:164:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 164 | _M_realloc_insert(begin() + (__position - cbegin()), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:664:43: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:672:47: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:113:33, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:116:32, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: -/usr/include/c++/12/bits/stl_vector.h:1561:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1561 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1481:22, - inlined from 'static void boost::python::vector_indexing_suite::set_slice(Container&, index_type, index_type, Iter, Iter) [with Iter = __gnu_cxx::__normal_iterator >; Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:117:33, - inlined from 'static void boost::python::detail::slice_helper::base_set_slice(Container&, PySliceObject*, PyObject*) [with Container = std::vector; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>; ProxyHandler = boost::python::detail::no_proxy_helper, boost::python::detail::final_vector_derived_policies, true>, boost::python::detail::container_element, unsigned int, boost::python::detail::final_vector_derived_policies, true> >, unsigned int>; Data = long long unsigned int; Index = unsigned int]' at /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:685:47: -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 1779 | _M_range_insert(__pos, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - 1780 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_vector.h:1779:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 87%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +[ 96%] Linking CXX executable molTautomerTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Built target rxnTestCatch -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend +[ 96%] Built target molTautomerTest +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.cpp -[ 87%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp +[ 96%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -15658,14 +16429,14 @@ from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:25, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.h:20, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.cpp:10: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -15675,153 +16446,65 @@ from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/smart_ptr.hpp:19, from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:34: + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:33: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 523 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2541:27: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2542:21: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2543:21: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2544:21: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:55:25, - inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2551:27: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2552:21: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:129:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Conformer.h:136:22, - inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp:2553:21: -/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1032 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Metal.cpp -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Normalize.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/Geometry/point.h:16: -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:175:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 175 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', - inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: -/usr/include/boost/smart_ptr/shared_ptr.hpp:416:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] - 416 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) - | ~~^~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here - 129 | ROMOL_SPTR react = python::extract(reactant); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:17: -In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', - inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:416:72, - inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: -/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] - 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) - | ~~^~~ -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp: In function 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]': -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here - 129 | ROMOL_SPTR react = python::extract(reactant); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, - inlined from 'void RDKit::RDProps::clearComputedProps() const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:154:25, - inlined from 'void RDKit::MolClearComputedProps(const RDOb&) [with RDOb = ChemicalReaction]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/props.hpp:157:25: -/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1530 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:321:20, - inlined from 'void RDKit::RDProps::clearProp(const std::string&) const' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDProps.h:146:21, - inlined from 'void RDKit::MolClearProp(const RDOb&, const char*) [with RDOb = ChemicalReaction]' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/props.hpp:152:16: -/usr/include/c++/12/bits/stl_vector.h:1530:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1530 | { return _M_erase(begin() + (__position - cbegin())); } - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Validate.cpp -[ 88%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 96%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 88%] Built target testReaction +[ 96%] Built target tautomerQueryTestCatch make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +[ 96%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, @@ -15833,21 +16516,70 @@ /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 89%] Built target rdChemReactions +[ 97%] Built target rdTautomerQuery make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +[ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Charge.cpp +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp +[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/object/class.hpp:9, + from /usr/include/boost/python/class.hpp:13, + from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, + from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp In file included from /usr/include/c++/12/vector:70, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, @@ -16013,26 +16745,6 @@ /usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void test3()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:875:23: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void test3()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:876:23: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.cpp In file included from /usr/include/c++/12/vector:70, from /usr/include/catch2/catch.hpp:566, from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:10: @@ -16565,70 +17277,18 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, - inlined from 'void test14BWPalette()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:2981:22: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /usr/include/c++/12/functional:62, - from /usr/include/boost/function.hpp:23, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 89%] Built target moldraw2DTest1 -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Fragment.cpp -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, - inlined from 'void C_A_T_C_H_T_E_S_T_205()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:4509:20: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::setMonochromeMode(MolDrawOptions&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:530:28, - inlined from 'void RDKit::setMonochromeMode(MolDraw2D&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:539:20, - inlined from 'void C_A_T_C_H_T_E_S_T_164()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:3706:22: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void test3()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:875:23: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 532 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::setMonochromeMode(MolDrawOptions&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:530:28, - inlined from 'void RDKit::setMonochromeMode(MolDraw2D&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:539:20, - inlined from 'void C_A_T_C_H_T_E_S_T_164()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:3721:22: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void test3()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:876:23: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 531 | std::forward_as_tuple(std::move(__k)), @@ -16655,26 +17315,42 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Linking CXX executable moldraw2DRxnTest1 +[ 98%] Linking CXX executable moldraw2DRxnTest1 cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 89%] Built target moldraw2DRxnTest1 +[ 98%] Built target moldraw2DRxnTest1 make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +[ 98%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]', - inlined from 'void C_A_T_C_H_T_E_S_T_63()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:1292:25: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +[ 98%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 98%] Built target rdMolStandardize +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, + inlined from 'void test14BWPalette()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:2981:22: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -16693,36 +17369,56 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp -[ 90%] Linking CXX executable moldraw2DTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 90%] Built target moldraw2DTestCatch -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 90%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/catch_tests.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp -[ 90%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, + inlined from 'void C_A_T_C_H_T_E_S_T_205()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:4509:20: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[ 98%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 90%] Built target molHashCatchTest -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend +[ 98%] Built target moldraw2DTest1 +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 90%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp +[ 99%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::setMonochromeMode(MolDrawOptions&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:530:28, + inlined from 'void RDKit::setMonochromeMode(MolDraw2D&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:539:20, + inlined from 'void C_A_T_C_H_T_E_S_T_164()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:3706:22: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::setMonochromeMode(MolDrawOptions&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:530:28, + inlined from 'void RDKit::setMonochromeMode(MolDraw2D&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:539:20, + inlined from 'void C_A_T_C_H_T_E_S_T_164()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:3721:22: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]', + inlined from 'void C_A_T_C_H_T_E_S_T_63()' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:1292:25: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/vector:70, from /usr/include/c++/12/functional:62, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -17211,756 +17907,69 @@ /usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:116:13: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:117:13: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:118:13: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:119:13: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:120:12: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:121:14: -/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 531 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 532 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = RDGeom::Point2D; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1668:20, - inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = RDGeom::Point2D; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:706:23, - inlined from 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDGeom::Point2D]' at /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:140:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1668:20, - inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:706:23, - inlined from 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:140:15: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 91%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so 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'/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 91%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/deprotectTest.cpp -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 93%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target rdMolDraw2D -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp:32: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp -[ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target rdDeprotect -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp:32: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target testRGroupDecomp -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp -[ 93%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target testRGroupDecompInternals -make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp:34: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX executable rgroupCatchTests -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target rgroupCatchTests -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp -In file included from /usr/include/c++/12/vector:70, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/RDLog.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h:14, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target MolStandardize -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 93%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitga.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target rdRGroupDecomposition -make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC 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../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target rdMolEnumerator -make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/test1.cpp -[ 93%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 93%] Built target testMolEnumerator -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testNormalize.cpp -[ 94%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 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Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testValidate.cpp -[ 94%] Linking CXX executable molNormalizeTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 94%] Built target molNormalizeTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testCharge.cpp -[ 94%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so 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'/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testTautomer.cpp -[ 95%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 95%] Built target molValidateTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/test2.cpp -[ 96%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 96%] Built target molChargeTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/testFragment.cpp -[ 96%] Linking CXX executable molStandardizeSmallTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeSmallTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -o molStandardizeSmallTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 96%] Built target molStandardizeSmallTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/catch_tests.cpp -[ 96%] Linking CXX executable molFragmentTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 96%] Built target molFragmentTest -make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp -In file included from /usr/include/c++/12/vector:70, - from /usr/include/catch2/catch.hpp:566, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/catch_tests.cpp:10: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Dict.h:271:20: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable molTautomerTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 96%] Built target molTautomerTest -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp -[ 97%] Linking CXX executable molStandardizeCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 97%] Built target molStandardizeCatchTest -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 97%] Built target ScaffoldNetwork -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/catch_tests.cpp -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 97%] Built target tautomerQueryTestCatch -make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/reproducible-path/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/object/class.hpp:9, - from /usr/include/boost/python/class.hpp:13, - from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, - from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[ 99%] Built target rdTautomerQuery -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[100%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp -[100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:116:13: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:117:13: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:118:13: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:119:13: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:120:12: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignCDKPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:121:14: +/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 531 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 532 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +[100%] Linking CXX executable moldraw2DTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[100%] Built target rdMolStandardize +[100%] Built target moldraw2DTestCatch make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= @@ -17969,6 +17978,30 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [100%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = RDGeom::Point2D; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1668:20, + inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = RDGeom::Point2D; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:706:23, + inlined from 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = RDGeom::Point2D]' at /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:140:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1668:20, + inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:706:23, + inlined from 'std::unique_ptr > pythonObjectToVect(const boost::python::api::object&) [with T = double]' at /build/reproducible-path/rdkit-202209.3/Code/RDBoost/Wrap.h:140:15: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -17987,8 +18020,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp [100%] Linking CXX executable testScaffoldNetwork cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -18007,20 +18038,20 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp -[100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +[100%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[100%] Built target rdScaffoldNetwork +[100%] Built target rdMolDraw2D make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= @@ -18029,6 +18060,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' [100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp +[100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[100%] Built target rdScaffoldNetwork +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -18047,8 +18085,16 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp +[100%] Linking CXX executable substructLibraryCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[100%] Built target substructLibraryCatchTest +[100%] Linking CXX executable substructLibraryTest +cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' +[100%] Built target substructLibraryTest In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -18067,16 +18113,6 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[100%] Linking CXX executable substructLibraryCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[100%] Built target substructLibraryCatchTest -[100%] Linking CXX executable substructLibraryTest -cd /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/arm-linux-gnueabihf/libboost_serialization.so ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -[100%] Built target substructLibraryTest /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp: In member function 'unsigned int RDKit::SubstructLibraryWrap::countMatches(const Query&, unsigned int, unsigned int, bool, bool, bool, int) const [with Query = RDKit::MolBundle]': /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:153:16: warning: infinite recursion detected [-Winfinite-recursion] 153 | unsigned int countMatches(const Query &query, unsigned int startIdx, @@ -18328,69 +18364,69 @@ Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Fonts +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/Demo +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemTransforms -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DetermineBonds -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/tutorial Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/tutorial +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/GenericGroups +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StructChecker Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Substruct +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/libs +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Test -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Trajectory -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/libs -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Fonts -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Qt/Demo -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolInterchange Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DetermineBonds +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Subgraphs Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/Query Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/Data +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers @@ -18400,8 +18436,8 @@ Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/RDBoost Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/DistGeom Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ForceField -Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF +Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/Numerics Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment Searching for files in directory /build/reproducible-path/rdkit-202209.3/Code/Numerics/EigenSolvers @@ -19311,6 +19347,8 @@ Generating code for file Feature.h... Generating code for file Contrib.h... Generating code for file ForceField.h... +Generating code for file OopBend.h... +Generating code for file StretchBend.h... Generating code for file AngleBend.h... Generating code for file AngleBend.h... Generating code for file AngleConstraint.h... @@ -19321,19 +19359,17 @@ Generating code for file Contribs.h... Generating code for file DistanceConstraint.h... Generating code for file DistanceConstraint.h... +Generating code for file Inversion.h... Generating code for file Nonbonded.h... Generating code for file Nonbonded.h... -Generating code for file OopBend.h... Generating code for file Params.h... Generating code for file Params.h... Generating code for file PositionConstraint.h... Generating code for file PositionConstraint.h... -Generating code for file StretchBend.h... Generating code for file TorsionAngle.h... Generating code for file TorsionAngle.h... Generating code for file TorsionConstraint.h... Generating code for file TorsionConstraint.h... -Generating code for file Inversion.h... Generating code for file Grid3D.h... Generating code for file GridUtils.h... Generating code for file point.h... @@ -19424,6 +19460,8 @@ Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... +Generating code for file details.h... +Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... @@ -19477,11 +19515,11 @@ Generating code for file TorsionAngleM6.h... Generating code for file TorsionPreferences.h... Generating code for file FFConvenience.h... +Generating code for file MMFF.h... Generating code for file AtomTyper.h... Generating code for file AtomTyper.h... Generating code for file Builder.h... Generating code for file Builder.h... -Generating code for file MMFF.h... Generating code for file UFF.h... Generating code for file FragCatalogEntry.h... Generating code for file FragCatalogUtils.h... @@ -19534,8 +19572,6 @@ Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.h... -Generating code for file details.h... -Generating code for file details.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... @@ -19550,6 +19586,8 @@ Generating code for file Metal.h... Generating code for file MolStandardize.h... Generating code for file Normalize.h... +Generating code for file Tautomer.h... +Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... @@ -19603,8 +19641,6 @@ Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... -Generating code for file Tautomer.h... -Generating code for file Tautomer.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... @@ -19710,6 +19746,8 @@ Generating docs for file Feature.h... Generating docs for file Contrib.h... Generating docs for file ForceField.h... +Generating docs for file OopBend.h... +Generating docs for file StretchBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleBend.h... Generating docs for file AngleConstraint.h... @@ -19720,19 +19758,17 @@ Generating docs for file Contribs.h... Generating docs for file DistanceConstraint.h... Generating docs for file DistanceConstraint.h... +Generating docs for file Inversion.h... Generating docs for file Nonbonded.h... Generating docs for file Nonbonded.h... -Generating docs for file OopBend.h... Generating docs for file Params.h... Generating docs for file Params.h... Generating docs for file PositionConstraint.h... Generating docs for file PositionConstraint.h... -Generating docs for file StretchBend.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionAngle.h... Generating docs for file TorsionConstraint.h... Generating docs for file TorsionConstraint.h... -Generating docs for file Inversion.h... Generating docs for file Grid3D.h... Generating docs for file GridUtils.h... Generating docs for file point.h... @@ -19823,6 +19859,8 @@ Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... +Generating docs for file details.h... +Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... @@ -19871,18 +19909,16 @@ Generating docs for file SeedSet.h... Generating docs for file SubstructMatchCustom.h... Generating docs for file SubstructureCache.h... -Generating/build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' -/build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' - docs for file Target.h... +Generating docs for file Target.h... Generating docs for file TargetMatch.h... Generating docs for file TorsionAngleM6.h... Generating docs for file TorsionPreferences.h... Generating docs for file FFConvenience.h... +Generating docs for file MMFF.h... Generating docs for file AtomTyper.h... Generating docs for file AtomTyper.h... Generating docs for file Builder.h... Generating docs for file Builder.h... -Generating docs for file MMFF.h... Generating docs for file UFF.h... Generating docs for file FragCatalogEntry.h... Generating docs for file FragCatalogUtils.h... @@ -19935,8 +19971,6 @@ Generating docs for file mf.h... Generating docs for file MolHash.h... Generating docs for file nmmolhash.h... -Generating docs for file details.h... -Generating docs for file details.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... @@ -19951,6 +19985,8 @@ Generating docs for file Metal.h... Generating docs for file MolStandardize.h... Generating docs for file Normalize.h... +Generating docs for file Tautomer.h... +Generating docs for file Tautomer.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... @@ -19965,7 +20001,9 @@ Generating docs for file GasteigerParams.h... Generating docs for file PeriodicTable.h... Generating docs for file QueryAtom.h... -Generating docs for file QueryBond.h... +Generating docs for fi/build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' +/build/reproducible-path/rdkit-202209.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' +le QueryBond.h... Generating docs for file QueryOps.h... Generating docs for file RDKitBase.h... Generating docs for file RDKitQueries.h... @@ -20004,8 +20042,6 @@ Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... -Generating docs for file Tautomer.h... -Generating docs for file Tautomer.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... @@ -23599,7 +23635,7 @@ /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:1444: WARNING: None:any reference target not found: ./C++Examples/example15.cpp /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:1472: WARNING: None:any reference target not found: ./C++Examples/example16.cpp /build/reproducible-path/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:1510: WARNING: None:any reference target not found: ./C++Examples/example16.cpp -WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png%3Bbase64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png%3Bbase64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] +WARNING: Could not fetch remote image: https://img.shields.io/badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png%3Bbase64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC [HTTPSConnectionPool(host='img.shields.io', port=443): Max retries exceeded with url: /badge/Powered%20by-RDKit-3838ff.svg?logo=data:image/png%3Bbase64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQBAMAAADt3eJSAAAABGdBTUEAALGPC/xhBQAAACBjSFJNAAB6JgAAgIQAAPoAAACA6AAAdTAAAOpgAAA6mAAAF3CculE8AAAAFVBMVEXc3NwUFP8UPP9kZP+MjP+0tP////9ZXZotAAAAAXRSTlMAQObYZgAAAAFiS0dEBmFmuH0AAAAHdElNRQfmAwsPGi+MyC9RAAAAQElEQVQI12NgQABGQUEBMENISUkRLKBsbGwEEhIyBgJFsICLC0iIUdnExcUZwnANQWfApKCK4doRBsKtQFgKAQC5Ww1JEHSEkAAAACV0RVh0ZGF0ZTpjcmVhdGUAMjAyMi0wMy0xMVQxNToyNjo0NyswMDowMDzr2J4AAAAldEVYdGRhdGU6bW9kaWZ5ADIwMjItMDMtMTFUMTU6MjY6NDcrMDA6MDBNtmAiAAAAAElFTkSuQmCC (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -3] Temporary failure in name resolution'))] done writing... /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known /build/reproducible-path/rdkit-202209.3/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known @@ -26080,10 +26116,10 @@ /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202209.3 PYTHONPATH=/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf//lib:" PYTHONPATH=/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/:/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf//lib:" dh_auto_test - cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 + cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4 make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j3 +/usr/bin/ctest --force-new-ctest-process --verbose -j4 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -26114,12 +26150,44 @@ 3: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testDict 3: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral 3: Test timeout computed to be: 1500 -3: [10:19:49] Testing Github940: property dictionaries leaking memory -3: [10:19:49] done +test 4 + Start 4: testRDValue + +4: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testRDValue +4: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral +4: Test timeout computed to be: 1500 +3: [18:18:17] Testing Github940: property dictionaries leaking memory +3: [18:18:17] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect +4: -- running tests -- +4: min: -2147483648 -2147483648 +4: min: 0 0 +4: min: 2.22507e-308 2.22507e-308 +4: min: 1.17549e-38 1.17549e-38 +4: min: 0 0 +4: == int +4: == double +4: == float +4: == unsigned int +4: == bool +4: == std::string + 1/208 Test #4: testRDValue ............................ Passed 0.06 sec +test 5 + Start 5: testConcurrentQueue + +5: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testConcurrentQueue +5: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral +5: Test timeout computed to be: 1500 +5: [18:18:17] +5: ----------------------------------------- +5: [18:18:17] Finished: testPushAndPop() +5: [18:18:17] +5: ----------------------------------------- +5: [18:18:17] +5: ----------------------------------------- 1: core 1: RDKit 2D 1: @@ -26845,46 +26913,7 @@ 1: 10 2 1 0 1: M END 1: - 1/208 Test #1: testCoordGen ........................... Passed 0.89 sec -test 4 - Start 4: testRDValue - -4: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testRDValue -4: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral -4: Test timeout computed to be: 1500 -4: -- running tests -- -4: min: -2147483648 -2147483648 -4: min: 0 0 -4: min: 2.22507e-308 2.22507e-308 -4: min: 1.17549e-38 1.17549e-38 -4: min: 0 0 -4: == int -4: == double -4: == float -4: == unsigned int -4: == bool -4: == std::string - 2/208 Test #4: testRDValue ............................ Passed 0.02 sec -test 5 - Start 5: testConcurrentQueue - -5: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testConcurrentQueue -5: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral -5: Test timeout computed to be: 1500 -5: [10:19:50] -5: ----------------------------------------- -5: [10:19:50] Finished: testPushAndPop() -5: [10:19:50] -5: ----------------------------------------- -5: [10:19:50] -5: ----------------------------------------- -3: static boost any:1.04176 s -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.121s -2: -2: OK - 3/208 Test #2: pyCoordGen ............................. Passed 1.53 sec + 2/208 Test #1: testCoordGen ........................... Passed 2.53 sec test 6 Start 6: dictTestsCatch @@ -26894,26 +26923,26 @@ 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: - 4/208 Test #6: dictTestsCatch ......................... Passed 0.03 sec + 3/208 Test #6: dictTestsCatch ......................... Passed 0.05 sec test 7 Start 7: logTestsCatch 7: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral/logTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/RDGeneral 7: Test timeout computed to be: 1500 -7: [10:19:51] should not be silent -7: [10:19:51] should not be silent -7: [10:19:51] should not be silent -7: [10:19:51] should not be silent -7: [10:19:51] should not be silent -7: [10:19:51] should not be silent -7: [10:19:51] should not be silent -7: [10:19:51] should not be silent -7: [10:19:51] should not be silent +7: [18:18:19] should not be silent +7: [18:18:19] should not be silent +7: [18:18:19] should not be silent +7: [18:18:19] should not be silent +7: [18:18:19] should not be silent +7: [18:18:19] should not be silent +7: [18:18:19] should not be silent +7: [18:18:19] should not be silent +7: [18:18:19] should not be silent 7: =============================================================================== 7: All tests passed (24 assertions in 2 test cases) 7: - 5/208 Test #7: logTestsCatch .......................... Passed 0.03 sec + 4/208 Test #7: logTestsCatch .......................... Passed 0.07 sec test 8 Start 8: testDataStructs @@ -26936,62 +26965,34 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except - 6/208 Test #8: testDataStructs ........................ Passed 0.03 sec + 5/208 Test #8: testDataStructs ........................ Passed 0.09 sec test 9 Start 9: testFPB 9: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/testFPB 9: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs 9: Test timeout computed to be: 1500 - 7/208 Test #9: testFPB ................................ Passed 0.03 sec + 6/208 Test #9: testFPB ................................ Passed 0.09 sec test 10 Start 10: testMultiFPB 10: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/testMultiFPB 10: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs 10: Test timeout computed to be: 1500 - 8/208 Test #10: testMultiFPB ........................... Passed 0.04 sec + 7/208 Test #10: testMultiFPB ........................... Passed 0.19 sec test 11 Start 11: pyBV 11: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testBV.py" 11: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap 11: Test timeout computed to be: 1500 -3: dynamic boost any:2.87868 s -3: static RDAny:0.098292 s -3: dynamic RDAny:1.2846 s -3: static RDValue:9e-06 s -3: dynamic RDValue:0.11556 s -3: deleted! -3: [10:19:55] ------------------------------------- -3: [10:19:55] Testing String Pickle Roundtrips. -3: [10:19:55] done -3: [10:19:55] ------------------------------------- -3: [10:19:55] Testing conversion of vect to string. -3: [10:19:55] done -3: [10:19:55] ------------------------------------- -3: [10:19:55] Testing returning const references. -3: [10:19:55] any cast -3: [10:19:55] done: 0.002286 300000 -3: [10:19:55] copy -3: [10:19:55] done: 0.002187 300000 -3: [10:19:55] ref -3: [10:19:55] done: 0.002187 300000 -3: [10:19:55] dict -3: [10:19:55] done: 0.014438 300000 -3: [10:19:55] ref with hasVal -3: [10:19:55] done: 0.006126 300000 -3: [10:19:55] done -3: [10:19:55] ------------------------------------- -3: [10:19:55] Testing dict update. -3: [10:19:55] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! - 9/208 Test #3: testDict ............................... Passed 5.61 sec +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.457s +2: +2: OK +3: static boost any:0.751937 s + 8/208 Test #2: pyCoordGen ............................. Passed 4.52 sec test 12 Start 12: pyDiscreteValueVect @@ -27000,10 +27001,10 @@ 12: Test timeout computed to be: 1500 12: ...... 12: ---------------------------------------------------------------------- -12: Ran 6 tests in 0.009s +12: Ran 6 tests in 0.029s 12: 12: OK - 10/208 Test #12: pyDiscreteValueVect .................... Passed 0.94 sec + 9/208 Test #12: pyDiscreteValueVect .................... Passed 2.46 sec test 13 Start 13: pySparseIntVect @@ -27012,22 +27013,24 @@ 13: Test timeout computed to be: 1500 13: ......... 13: ---------------------------------------------------------------------- -13: Ran 9 tests in 0.025s +13: Ran 9 tests in 0.112s 13: 13: OK - 11/208 Test #13: pySparseIntVect ........................ Passed 0.72 sec + 10/208 Test #13: pySparseIntVect ........................ Passed 3.12 sec test 14 Start 14: pyFPB 14: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/testFPB.py" 14: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 +3: dynamic boost any:1.53624 s 14: ......... 14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.013s +14: Ran 9 tests in 0.126s 14: 14: OK - 12/208 Test #14: pyFPB .................................. Passed 0.68 sec +3: static RDAny:0.059713 s + 11/208 Test #14: pyFPB .................................. Passed 3.36 sec test 15 Start 15: testTransforms @@ -27042,8 +27045,8 @@ 15: testPointOps2D 15: **************************************** 15: test12D -15: ref1: 0.0146168 0.737715 ref2: 3.91872 4.1111 -15: pt1: 3.12101 0.556782 pt2: 2.76255 3.12061 +15: ref1: 4.1487 3.24251 ref2: 0.770861 1.56881 +15: pt1: 4.44937 3.59367 pt2: 1.00739 2.44161 15: **************************************** 15: test23D 15: **************************************** @@ -27058,7 +27061,7 @@ 15: **************************************** 15: testFromQuaternion 15: **************************************** - 13/208 Test #15: testTransforms ......................... Passed 0.02 sec + 12/208 Test #15: testTransforms ......................... Passed 0.09 sec test 16 Start 16: testGrid @@ -27082,7 +27085,7 @@ 16: --------------------------------- 16: testUniformGridIndexing 16: - 14/208 Test #16: testGrid ............................... Passed 0.12 sec + 13/208 Test #16: testGrid ............................... Passed 0.49 sec test 17 Start 17: geometryTestsCatch @@ -27092,7 +27095,7 @@ 17: =============================================================================== 17: All tests passed (50 assertions in 5 test cases) 17: - 15/208 Test #17: geometryTestsCatch ..................... Passed 0.03 sec + 14/208 Test #17: geometryTestsCatch ..................... Passed 0.09 sec test 18 Start 18: testPyGeometry @@ -27101,39 +27104,67 @@ 18: Test timeout computed to be: 1500 18: ........... 18: ---------------------------------------------------------------------- -18: Ran 11 tests in 0.103s +18: Ran 11 tests in 0.515s 18: 18: OK 18: Testing Geometry wrapper - 16/208 Test #18: testPyGeometry ......................... Passed 0.79 sec +3: dynamic RDAny:0.737226 s +3: static RDValue:1e-06 s +3: dynamic RDValue:0.043936 s +3: deleted! +3: [18:18:35] ------------------------------------- +3: [18:18:35] Testing String Pickle Roundtrips. +3: [18:18:35] done +3: [18:18:35] ------------------------------------- +3: [18:18:35] Testing conversion of vect to string. +3: [18:18:35] done +3: [18:18:35] ------------------------------------- +3: [18:18:35] Testing returning const references. +3: [18:18:35] any cast +3: [18:18:35] done: 0.001083 300000 +3: [18:18:35] copy +3: [18:18:35] done: 0.001047 300000 +3: [18:18:35] ref +3: [18:18:35] done: 0.001044 300000 +3: [18:18:35] dict +3: [18:18:35] done: 0.008773 300000 +3: [18:18:35] ref with hasVal +3: [18:18:35] done: 0.002861 300000 +3: [18:18:35] done +3: [18:18:35] ------------------------------------- +3: [18:18:35] Testing dict update. +3: [18:18:35] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! + 15/208 Test #3: testDict ............................... Passed 17.96 sec test 19 Start 19: testMatrices 19: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/testMatrices 19: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics 19: Test timeout computed to be: 1500 -19: [10:19:58] ----------------------------------------- -19: [10:19:58] Testing RDNumerics: vectors and matrices Code -19: [10:19:58] --------------------------------------- -19: [10:19:58] test1Vector -19: [10:19:58] --------------------------------------- -19: [10:19:58] test2Matrix -19: [10:19:58] --------------------------------------- -19: [10:19:58] test3SquareMatrix -19: [10:19:58] --------------------------------------- -19: [10:19:58] test4SymmMatrix - 17/208 Test #19: testMatrices ........................... Passed 0.01 sec +19: [18:18:35] ----------------------------------------- +19: [18:18:35] Testing RDNumerics: vectors and matrices Code +19: [18:18:35] --------------------------------------- +19: [18:18:35] test1Vector +19: [18:18:35] --------------------------------------- +19: [18:18:35] test2Matrix +19: [18:18:35] --------------------------------------- +19: [18:18:35] test3SquareMatrix +19: [18:18:35] --------------------------------------- +19: [18:18:35] test4SymmMatrix + 16/208 Test #19: testMatrices ........................... Passed 0.05 sec test 20 Start 20: testConrec 20: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/testConrec 20: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics 20: Test timeout computed to be: 1500 -20: =============================================================================== -20: test cases: 1 | 1 passed -20: assertions: - none - -20: - 18/208 Test #20: testConrec ............................. Passed 0.09 sec + 17/208 Test #18: testPyGeometry ......................... Passed 3.94 sec test 21 Start 21: testAlignment @@ -27151,13 +27182,89 @@ 21: --------------------------------------- 21: testReflection 21: --------------------------------------- - 19/208 Test #21: testAlignment .......................... Passed 0.03 sec + 18/208 Test #21: testAlignment .......................... Passed 0.07 sec test 22 Start 22: pyAlignment 22: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py" 22: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap 22: Test timeout computed to be: 1500 +20: =============================================================================== +20: test cases: 1 | 1 passed +20: assertions: - none - +20: + 19/208 Test #20: testConrec ............................. Passed 0.30 sec +test 23 + Start 23: testOptimizer + +23: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/testOptimizer +23: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer +23: Test timeout computed to be: 1500 +23: ------------------------------------- +23: Testing linear search. +23: done +23: ------------------------------------- +23: Testing BFGS optimization. +23: done + 20/208 Test #23: testOptimizer .......................... Passed 0.05 sec +test 24 + Start 24: testUFFForceField + +24: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF/testUFFForceField +24: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF +24: Test timeout computed to be: 1500 +24: ------------------------------------- +24: Unit tests for force field basics. +24: done +24: ------------------------------------- +24: Unit tests for basics of UFF bond-stretch terms. +24: done +24: ------------------------------------- +24: Unit tests for UFF bond-stretch terms. +24: done +24: ------------------------------------- +24: Unit tests for basics of UFF angle terms. +24: done +24: ------------------------------------- +24: Unit tests for UFF angle-bend terms. +24: theta = 3.14159; theta0 = 3.14159 +24: theta = 2.094395, param1.theta0 = 2.094395 +24: done +24: ------------------------------------- +24: Test Simple UFF molecule optimizations. +24: done +24: ------------------------------------- +24: Unit tests for UFF nonbonded terms. +24: done +24: ------------------------------------- +24: Test UFF torsional terms. +24: done +24: ------------------------------------- +24: Test UFF Parameter objects +24: ------------------------------------- +24: Test Simple UFF molecule optimization, part 2. +24: done +24: ------------------------------------- +24: Test UFF Torsion Conflicts. +24: C 0.4783 -0.7477 -0.0753 +24: C -0.5465 -0.0176 0.3519 +24: C -0.5114 1.4472 0.0870 +24: H -1.5201 -0.4838 0.2485 +24: H 0.4696 1.8363 0.3367 +24: O -1.2618 1.9423 0.6934 +24: F -0.7163 1.6298 -0.9622 +24: done +24: ------------------------------------- +24: Unit tests for UFF distance constraint terms. +24: done +24: ------------------------------------- +24: Unit tests for all UFF constraint terms. +24: done +24: ------------------------------------- +24: Unit tests for copying UFF ForceFields. +24: done +24: ------------------------------------- +24: Unit test for UFF butane scan. 22: EEE.. 22: ====================================================================== 22: ERROR: test1Basic (__main__.TestCase.test1Basic) @@ -27202,11 +27309,11 @@ 22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 22: 22: ---------------------------------------------------------------------- -22: Ran 5 tests in 0.009s +22: Ran 5 tests in 0.020s 22: 22: FAILED (errors=3) 22: Testing Alignment Wrapper code: - 20/208 Test #22: pyAlignment ............................***Failed 0.69 sec + 21/208 Test #22: pyAlignment ............................***Failed 2.56 sec EEE.. ====================================================================== ERROR: test1Basic (__main__.TestCase.test1Basic) @@ -27251,84 +27358,11 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 5 tests in 0.009s +Ran 5 tests in 0.020s FAILED (errors=3) Testing Alignment Wrapper code: -test 23 - Start 23: testOptimizer - -23: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/testOptimizer -23: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer -23: Test timeout computed to be: 1500 -23: ------------------------------------- -23: Testing linear search. -23: done -23: ------------------------------------- -23: Testing BFGS optimization. -23: done - 21/208 Test #23: testOptimizer .......................... Passed 0.01 sec -test 24 - Start 24: testUFFForceField - -24: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF/testUFFForceField -24: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF -24: Test timeout computed to be: 1500 -24: ------------------------------------- -24: Unit tests for force field basics. -24: done -24: ------------------------------------- -24: Unit tests for basics of UFF bond-stretch terms. -24: done -24: ------------------------------------- -24: Unit tests for UFF bond-stretch terms. -24: done -24: ------------------------------------- -24: Unit tests for basics of UFF angle terms. -24: done -24: ------------------------------------- -24: Unit tests for UFF angle-bend terms. -24: theta = 3.14159; theta0 = 3.14159 -24: theta = 2.094395, param1.theta0 = 2.094395 -24: done -24: ------------------------------------- -24: Test Simple UFF molecule optimizations. -24: done -24: ------------------------------------- -24: Unit tests for UFF nonbonded terms. -24: done -24: ------------------------------------- -24: Test UFF torsional terms. -24: done -24: ------------------------------------- -24: Test UFF Parameter objects -24: ------------------------------------- -24: Test Simple UFF molecule optimization, part 2. -24: done -24: ------------------------------------- -24: Test UFF Torsion Conflicts. -24: C 0.4783 -0.7477 -0.0753 -24: C -0.5465 -0.0176 0.3519 -24: C -0.5114 1.4472 0.0870 -24: H -1.5201 -0.4838 0.2485 -24: H 0.4696 1.8363 0.3367 -24: O -1.2618 1.9423 0.6934 -24: F -0.7163 1.6298 -0.9622 -24: done -24: ------------------------------------- -24: Unit tests for UFF distance constraint terms. -24: done -24: ------------------------------------- -24: Unit tests for all UFF constraint terms. -24: done -24: ------------------------------------- -24: Unit tests for copying UFF ForceFields. -24: done -24: ------------------------------------- -24: Unit test for UFF butane scan. -24: done - 22/208 Test #24: testUFFForceField ...................... Passed 0.98 sec test 25 Start 25: testMMFFForceField @@ -27337,23 +27371,19 @@ 25: Test timeout computed to be: 1500 25: ------------------------------------- 25: Official MMFF validation suite. -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -11: .................. -11: ---------------------------------------------------------------------- -11: Ran 18 tests in 13.512s -11: -11: OK - 23/208 Test #11: pyBV ................................... Passed 14.21 sec +24: done + 22/208 Test #24: testUFFForceField ...................... Passed 2.77 sec test 26 Start 26: pyForceFieldConstraints 26: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/ForceField/Wrap/testConstraints.py" 26: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap 26: Test timeout computed to be: 1500 -26: ...[10:20:06] Warning: molecule is tagged as 3D, but all Z coords are zero -26: [10:20:06] Molecule does not have explicit Hs. Consider calling AddHs() -26: [10:20:06] +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +26: ...[18:18:42] Warning: molecule is tagged as 3D, but all Z coords are zero +26: [18:18:42] Molecule does not have explicit Hs. Consider calling AddHs() +26: [18:18:42] 26: 26: **** 26: Invariant Violation @@ -27362,9 +27392,9 @@ 26: Failed Expression: status >= 0 26: **** 26: -26: ......[10:20:07] Warning: molecule is tagged as 3D, but all Z coords are zero -26: [10:20:07] Molecule does not have explicit Hs. Consider calling AddHs() -26: [10:20:07] +26: ......[18:18:43] Warning: molecule is tagged as 3D, but all Z coords are zero +26: [18:18:43] Molecule does not have explicit Hs. Consider calling AddHs() +26: [18:18:43] 26: 26: **** 26: Invariant Violation @@ -27375,10 +27405,10 @@ 26: 26: ... 26: ---------------------------------------------------------------------- -26: Ran 12 tests in 0.893s +26: Ran 12 tests in 2.181s 26: 26: OK - 24/208 Test #26: pyForceFieldConstraints ................ Passed 1.78 sec + 23/208 Test #26: pyForceFieldConstraints ................ Passed 6.08 sec test 27 Start 27: testDistGeom @@ -27396,7 +27426,7 @@ 27: 1 1 1 0 27: *********************************************************** 27: - 25/208 Test #27: testDistGeom ........................... Passed 0.04 sec + 24/208 Test #27: testDistGeom ........................... Passed 0.16 sec test 28 Start 28: pyDistGeom @@ -27489,10 +27519,10 @@ 28: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 28: 28: ---------------------------------------------------------------------- -28: Ran 6 tests in 0.008s +28: Ran 6 tests in 0.039s 28: 28: FAILED (errors=6) - 26/208 Test #28: pyDistGeom .............................***Failed 0.63 sec + 25/208 Test #28: pyDistGeom .............................***Failed 2.99 sec EEEEEE ====================================================================== ERROR: test1SmoothPass (__main__.TestCase.test1SmoothPass) @@ -27579,7 +27609,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 6 tests in 0.008s +Ran 6 tests in 0.039s FAILED (errors=6) @@ -27598,7 +27628,7 @@ 29: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 29: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 29: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 -29: 8 22 Ti chg: 0 deg: 1 exp: [10:20:08] +29: 8 22 Ti chg: 0 deg: 1 exp: [18:18:47] 29: 29: **** 29: Pre-condition Violation @@ -27616,7 +27646,7 @@ 29: 4 5->6 order: 3 conj?: 0 aromatic?: 0 29: 5 6->7 order: 1 conj?: 0 aromatic?: 0 29: 6 7->8 order: 2 conj?: 0 aromatic?: 0 -29: [10:20:08] +29: [18:18:47] 29: 29: **** 29: Pre-condition Violation @@ -27625,7 +27655,7 @@ 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: -29: [10:20:08] +29: [18:18:47] 29: 29: **** 29: Pre-condition Violation @@ -27634,7 +27664,7 @@ 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: -29: [10:20:08] +29: [18:18:47] 29: 29: **** 29: Pre-condition Violation @@ -27643,7 +27673,7 @@ 29: Failed Expression: atomIdx1 != atomIdx2 29: **** 29: -29: [10:20:08] +29: [18:18:47] 29: 29: **** 29: Pre-condition Violation @@ -27652,7 +27682,7 @@ 29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 29: **** 29: -29: [10:20:08] +29: [18:18:47] 29: 29: **** 29: Pre-condition Violation @@ -27661,9 +27691,9 @@ 29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 29: **** 29: -29: [10:20:08] Explicit valence for atom # 0 B, 4, is greater than permitted -29: [10:20:08] Explicit valence for atom # 0 B, 5, is greater than permitted -29: [10:20:08] +29: [18:18:47] Explicit valence for atom # 0 B, 4, is greater than permitted +29: [18:18:47] Explicit valence for atom # 0 B, 5, is greater than permitted +29: [18:18:47] 29: 29: **** 29: Post-condition Violation @@ -27672,12 +27702,12 @@ 29: Failed Expression: anum > -1 29: **** 29: -29: [10:20:08] ------------------------------------- -29: [10:20:08] Test github381: thread-safe initialization of the periodic table -29: [10:20:08] done -29: [10:20:08] ------------------------------------- -29: [10:20:08] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [10:20:08] +29: [18:18:47] ------------------------------------- +29: [18:18:47] Test github381: thread-safe initialization of the periodic table +29: [18:18:48] done +29: [18:18:48] ------------------------------------- +29: [18:18:48] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [18:18:48] 29: 29: **** 29: Pre-condition Violation @@ -27686,7 +27716,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [10:20:08] +29: [18:18:48] 29: 29: **** 29: Pre-condition Violation @@ -27695,10 +27725,10 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [10:20:08] done -29: [10:20:08] ------------------------------------- -29: [10:20:08] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [10:20:08] +29: [18:18:48] done +29: [18:18:48] ------------------------------------- +29: [18:18:48] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [18:18:48] 29: 29: **** 29: Pre-condition Violation @@ -27707,7 +27737,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [10:20:08] +29: [18:18:48] 29: 29: **** 29: Pre-condition Violation @@ -27716,27 +27746,21 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [10:20:08] done -29: [10:20:08] ------------------------------------- -29: [10:20:08] Test github1453: RWMol.clear() should reset the numBonds count. -29: [10:20:08] done -29: [10:20:08] ------------------------------------- -29: [10:20:08] Test range-based for loops. -29: [10:20:08] done -29: [10:20:08] ------------------------------------- -29: [10:20:08] Test github1642: Atom index type is too low for big molecules. -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -25: All 191 tests passed -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -25: All 191 tests passed -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -5: [10:20:37] Finished: testMultipleTimes() -5: [10:20:37] -5: ----------------------------------------- - 27/208 Test #5: testConcurrentQueue .................... Passed 47.14 sec +29: [18:18:48] done +29: [18:18:48] ------------------------------------- +29: [18:18:48] Test github1453: RWMol.clear() should reset the numBonds count. +29: [18:18:48] done +29: [18:18:48] ------------------------------------- +29: [18:18:48] Test range-based for loops. +29: [18:18:48] done +29: [18:18:48] ------------------------------------- +29: [18:18:48] Test github1642: Atom index type is too low for big molecules. +11: .................. +11: ---------------------------------------------------------------------- +11: Ran 18 tests in 45.840s +11: +11: OK + 26/208 Test #11: pyBV ................................... Passed 48.57 sec test 30 Start 30: graphmolcpTest @@ -27747,45 +27771,46 @@ 30: 30: 30: COPY - 28/208 Test #30: graphmolcpTest ......................... Passed 0.10 sec +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... + 27/208 Test #30: graphmolcpTest ......................... Passed 0.19 sec test 31 Start 31: graphmolqueryTest 31: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolqueryTest 31: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 31: Test timeout computed to be: 1500 -31: [10:20:38] ---------------------- Test1 -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test2 -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test3 -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test4 -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test5 -31: [10:20:38] Done! -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test issue 2892580 -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test github issue 53: query molecules not matching [R] -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test queries using qualifiers instead of == -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test extra atom queries -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test extra bond queries -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test num heteroatom neighbor queries -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test atom type queries -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -31: [10:20:38] Done! -31: [10:20:38] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -31: [10:20:38] Done! - 29/208 Test #31: graphmolqueryTest ...................... Passed 0.12 sec +31: [18:19:09] ---------------------- Test1 +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test2 +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test3 +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test4 +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test5 +31: [18:19:09] Done! +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test issue 2892580 +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test github issue 53: query molecules not matching [R] +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test queries using qualifiers instead of == +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test extra atom queries +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test extra bond queries +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test num heteroatom neighbor queries +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test atom type queries +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +31: [18:19:09] Done! +31: [18:19:09] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +31: [18:19:09] Done! + 28/208 Test #31: graphmolqueryTest ...................... Passed 0.22 sec test 32 Start 32: graphmolMolOpsTest @@ -27796,18 +27821,19 @@ 32: 1 1 1 32: 2 1 0.75 32: path: 2 -32: [10:20:38] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. -32: [10:20:38] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. -32: [10:20:38] Explicit valence for atom # 0 B, 5, is greater than permitted -32: [10:20:38] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [10:20:38] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [10:20:38] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [10:20:38] Explicit valence for atom # 1 Si, 7, is greater than permitted +32: [18:19:09] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. +32: [18:19:09] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. +32: [18:19:09] Explicit valence for atom # 0 B, 5, is greater than permitted +32: [18:19:09] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [18:19:09] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [18:19:09] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [18:19:09] Explicit valence for atom # 1 Si, 7, is greater than permitted +25: All 191 tests passed 32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -32: [10:20:38] non-ring atom 0 marked aromatic -32: [10:20:38] non-ring atom 0 marked aromatic -32: [10:20:38] Conflicting single bond directions around double bond at index 17. -32: [10:20:38] BondStereo set to STEREONONE and single bond directions set to NONE. +32: [18:19:10] non-ring atom 0 marked aromatic +32: [18:19:10] non-ring atom 0 marked aromatic +32: [18:19:10] Conflicting single bond directions around double bond at index 17. +32: [18:19:10] BondStereo set to STEREONONE and single bond directions set to NONE. 32: starting ring finding 32: done 32: starting ring finding @@ -27824,28 +27850,26 @@ 32: starting ring finding 32: done 32: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -32: [10:20:38] WARNING: not removing hydrogen atom with dummy atom neighbors +32: [18:19:10] WARNING: not removing hydrogen atom with dummy atom neighbors 32: ------------------------------- -32: [10:20:38] Explicit valence for atom # 0 N, 4, is greater than permitted -32: [10:20:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [10:20:38] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -32: [10:20:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [10:20:38] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -32: [10:20:39] WARNING: not removing hydrogen atom with dummy atom neighbors -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -32: [10:20:40] Maximum BFS search size exceeded. -32: This is likely due to a highly symmetric fused ring system. -25: All 191 tests passed +32: [18:19:10] Explicit valence for atom # 0 N, 4, is greater than permitted +32: [18:19:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [18:19:10] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +32: [18:19:10] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [18:19:10] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -32: [10:20:41] Maximum BFS search size exceeded. +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +32: [18:19:10] WARNING: not removing hydrogen atom with dummy atom neighbors +32: [18:19:14] Maximum BFS search size exceeded. +32: This is likely due to a highly symmetric fused ring system. +32: [18:19:17] Maximum BFS search size exceeded. 32: This is likely due to a highly symmetric fused ring system. 32: F/C=C/Cl 32: [H]/C(F)=C(/[H])Cl 32: F/C=C/Cl 32: F/C=C/Cl 32: C/C(F)=C(/C)Cl - 30/208 Test #32: graphmolMolOpsTest ..................... Passed 3.56 sec + 29/208 Test #32: graphmolMolOpsTest ..................... Passed 9.23 sec test 33 Start 33: graphmoltestChirality @@ -27855,32 +27879,32 @@ 33: -------------------------- 33: -------------------------- 33: C/C=C/C(C)Cl -33: [10:20:41] Conflicting single bond directions around double bond at index 2. -33: [10:20:41] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [10:20:41] Conflicting single bond directions around double bond at index 4. -33: [10:20:41] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [10:20:41] Conflicting single bond directions around double bond at index 15. -33: [10:20:41] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [10:20:41] Conflicting single bond directions around double bond at index 2. -33: [10:20:41] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [10:20:41] Conflicting single bond directions around double bond at index 1. -33: [10:20:41] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [18:19:18] Conflicting single bond directions around double bond at index 2. +33: [18:19:18] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [18:19:18] Conflicting single bond directions around double bond at index 4. +33: [18:19:18] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [18:19:18] Conflicting single bond directions around double bond at index 15. +33: [18:19:18] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [18:19:18] Conflicting single bond directions around double bond at index 2. +33: [18:19:18] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [18:19:18] Conflicting single bond directions around double bond at index 1. +33: [18:19:18] BondStereo set to STEREONONE and single bond directions set to NONE. 33: -------------------------------------------------- - 31/208 Test #33: graphmoltestChirality .................. Passed 0.25 sec + 30/208 Test #33: graphmoltestChirality .................. Passed 0.61 sec test 34 Start 34: graphmoltestPickler 34: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmoltestPickler 34: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 34: Test timeout computed to be: 1500 -34: [10:20:41] ------------------------------------- -34: [10:20:41] Testing String Pickle Roundtrips. -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing reading existing pickle file (v2). -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing combining molecules using pickles. +34: [18:19:19] ------------------------------------- +34: [18:19:19] Testing String Pickle Roundtrips. +34: [18:19:19] done +34: [18:19:19] ------------------------------------- +34: [18:19:19] Testing reading existing pickle file (v2). +34: [18:19:19] done +34: [18:19:19] ------------------------------------- +34: [18:19:19] Testing combining molecules using pickles. 34: Atoms: 34: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 @@ -27897,37 +27921,37 @@ 34: 4 4->5 order: 1 conj?: 0 aromatic?: 0 34: 5 5->6 order: 1 conj?: 0 aromatic?: 0 34: 6 6->3 order: 1 conj?: 0 aromatic?: 0 -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing Issue164: Roundtrip Pickle Failure. -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing Issue219: Pickle Failure with Conformations. -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing Issue220: Pickle problems with bond stereochemistry. -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing query serialization. -34: [10:20:42] C=[$(C=O)] -34: [10:20:42] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing radical handling in pickles. -34: [10:20:42] done -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing sf.net issue 2788233. -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing sf.net issue 3202580. +34: [18:19:19] done +34: [18:19:19] ------------------------------------- +34: [18:19:19] Testing Issue164: Roundtrip Pickle Failure. +34: [18:19:19] done +34: [18:19:19] ------------------------------------- +34: [18:19:19] Testing Issue219: Pickle Failure with Conformations. +34: [18:19:19] done +34: [18:19:19] ------------------------------------- +34: [18:19:19] Testing Issue220: Pickle problems with bond stereochemistry. +34: [18:19:19] done +34: [18:19:19] ------------------------------------- +34: [18:19:19] Testing query serialization. +34: [18:19:20] C=[$(C=O)] +34: [18:19:20] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +34: [18:19:20] done +34: [18:19:20] ------------------------------------- +34: [18:19:20] Testing radical handling in pickles. +34: [18:19:20] done +34: [18:19:20] done +34: [18:19:20] ------------------------------------- +34: [18:19:20] Testing sf.net issue 2788233. +34: [18:19:20] done +34: [18:19:20] ------------------------------------- +34: [18:19:20] Testing sf.net issue 3202580. 34: mass! 13.0034 -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing sf.net issue 3316407. -34: [10:20:42] done -34: [10:20:42] ------------------------------------- -34: [10:20:42] Testing sf.net issue 3496759. +34: [18:19:20] done +34: [18:19:20] ------------------------------------- +34: [18:19:20] Testing sf.net issue 3316407. +34: [18:19:20] done +34: [18:19:20] ------------------------------------- +34: [18:19:20] Testing sf.net issue 3496759. 34: smi match: *C *C 34: smi match: **=* **=* 34: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -28354,157 +28378,145 @@ 34: smi match: * * 34: smi match: ***** ***** 34: smi match: NC(N)=O NC(N)=O -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing sf.net issue 280. -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing sf.net issue 285. -34: [10:20:43] done -34: [10:20:43] done -34: [10:20:43] done -34: [10:20:43] done -34: [10:20:43] done -34: [10:20:43] done -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing Github2441: Add RDProps interface to Conformers. -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing Issue2510: Pickle Confs as double. -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing loading pickled mols with conformers -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing conformer reading/writing options -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing property reading options -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing property reading options -34: [10:20:43] done -34: [10:20:43] ------------------------------------- -34: [10:20:43] Testing boost::serialization integration -34: [10:20:43] done - 32/208 Test #34: graphmoltestPickler .................... Passed 1.11 sec +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing sf.net issue 280. +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing sf.net issue 285. +34: [18:19:21] done +34: [18:19:21] done +34: [18:19:21] done +34: [18:19:21] done +34: [18:19:21] done +34: [18:19:21] done +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing Github2441: Add RDProps interface to Conformers. +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing Issue2510: Pickle Confs as double. +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing loading pickled mols with conformers +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing conformer reading/writing options +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing property reading options +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing property reading options +34: [18:19:21] done +34: [18:19:21] ------------------------------------- +34: [18:19:21] Testing boost::serialization integration +34: [18:19:21] done + 31/208 Test #34: graphmoltestPickler .................... Passed 2.57 sec test 35 Start 35: graphmoltestPicklerGlobalSetting 35: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmoltestPicklerGlobalSetting 35: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 35: Test timeout computed to be: 1500 -35: [10:20:43] done - 33/208 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.07 sec +35: [18:19:21] done + 32/208 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.16 sec test 36 Start 36: graphmolIterTest 36: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolIterTest 36: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 36: Test timeout computed to be: 1500 - 34/208 Test #36: graphmolIterTest ....................... Passed 0.07 sec + 33/208 Test #36: graphmolIterTest ....................... Passed 0.16 sec test 37 Start 37: hanoiTest 37: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/hanoiTest 37: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 37: Test timeout computed to be: 1500 - 35/208 Test #37: hanoiTest .............................. Passed 9.48 sec +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... + 34/208 Test #37: hanoiTest .............................. Passed 26.00 sec test 38 Start 38: graphmolMemTest1 38: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolMemTest1 38: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 38: Test timeout computed to be: 1500 - 36/208 Test #38: graphmolMemTest1 ....................... Passed 0.03 sec + 35/208 Test #38: graphmolMemTest1 ....................... Passed 0.10 sec test 39 Start 39: resMolSupplierTest 39: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/resMolSupplierTest 39: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 39: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -25: All 191 tests passed -25: done -25: ------------------------------------- -25: Unit tests for all MMFF constraint terms. -25: 10.0003 -25: done -25: ------------------------------------- -25: Unit test for MMFF TorsionConstraint close to 0 degrees. -25: done -25: ------------------------------------- -25: Unit tests for copying MMFF ForceFields. -25: done -25: ------------------------------------- -25: Unit test for MMFF butane scan. -25: done - 37/208 Test #25: testMMFFForceField ..................... Passed 61.74 sec + 36/208 Test #39: resMolSupplierTest ..................... Passed 45.06 sec test 40 Start 40: molBundleTest 40: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/molBundleTest 40: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 40: Test timeout computed to be: 1500 - 38/208 Test #40: molBundleTest .......................... Passed 0.07 sec + 37/208 Test #40: molBundleTest .......................... Passed 0.20 sec test 41 Start 41: testSGroup 41: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/testSGroup 41: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 41: Test timeout computed to be: 1500 - 39/208 Test #41: testSGroup ............................. Passed 0.11 sec + 38/208 Test #41: testSGroup ............................. Passed 0.35 sec test 42 Start 42: test-valgrind 42: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/test-valgrind 42: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 42: Test timeout computed to be: 1500 - 40/208 Test #42: test-valgrind .......................... Passed 0.06 sec + 39/208 Test #42: test-valgrind .......................... Passed 0.20 sec test 43 Start 43: graphmolTestsCatch 43: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolTestsCatch 43: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 43: Test timeout computed to be: 1500 -43: [10:21:02] WARNING: not removing hydrogen atom without neighbors -43: [10:21:02] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [10:21:02] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [10:21:02] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [10:21:02] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [10:21:02] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [10:21:02] Explicit valence for atom # 1 N, 6, is greater than permitted -43: [10:21:02] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [10:21:02] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [10:21:02] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [10:21:02] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [10:21:02] non-ring atom 2 marked aromatic -43: [10:21:02] non-ring atom 2 marked aromatic -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [10:21:02] Explicit valence for atom # 1 O, 3, is greater than permitted -43: [10:21:02] Explicit valence for atom # 4 F, 2, is greater than permitted -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 6 7 8 -43: [10:21:02] Explicit valence for atom # 1 C, 5, is greater than permitted -43: [10:21:02] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [10:21:02] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [10:21:02] WARNING: not removing hydrogen atom with wedged bond -43: [10:21:02] WARNING: not removing hydrogen atom without neighbors -43: [10:21:02] WARNING: not removing hydrogen atom without neighbors -43: [10:21:02] WARNING: not removing hydrogen atom without neighbors -43: [10:21:02] WARNING: not removing hydrogen atom without neighbors -43: [10:21:02] Unreasonable formal charge on hydrogen # 0. -43: [10:21:02] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [10:21:02] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [10:21:02] +43: [18:20:34] WARNING: not removing hydrogen atom without neighbors +43: [18:20:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [18:20:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [18:20:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [18:20:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [18:20:34] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [18:20:34] Explicit valence for atom # 1 N, 6, is greater than permitted +43: [18:20:34] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [18:20:34] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [18:20:34] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [18:20:34] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [18:20:34] non-ring atom 2 marked aromatic +43: [18:20:34] non-ring atom 2 marked aromatic +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [18:20:34] Explicit valence for atom # 1 O, 3, is greater than permitted +43: [18:20:34] Explicit valence for atom # 4 F, 2, is greater than permitted +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 6 7 8 +43: [18:20:34] Explicit valence for atom # 1 C, 5, is greater than permitted +43: [18:20:34] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [18:20:34] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [18:20:34] WARNING: not removing hydrogen atom with wedged bond +43: [18:20:34] WARNING: not removing hydrogen atom without neighbors +43: [18:20:34] WARNING: not removing hydrogen atom without neighbors +43: [18:20:34] WARNING: not removing hydrogen atom without neighbors +43: [18:20:34] WARNING: not removing hydrogen atom without neighbors +43: [18:20:34] Unreasonable formal charge on hydrogen # 0. +43: [18:20:34] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [18:20:34] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28513,7 +28525,7 @@ 43: Failed Expression: at 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28522,7 +28534,7 @@ 43: Failed Expression: at->hasOwningMol() 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28531,7 +28543,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28540,7 +28552,7 @@ 43: Failed Expression: at 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28549,7 +28561,7 @@ 43: Failed Expression: at->hasOwningMol() 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28558,7 +28570,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28567,7 +28579,7 @@ 43: Failed Expression: at 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28576,7 +28588,7 @@ 43: Failed Expression: at->hasOwningMol() 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28585,7 +28597,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28594,7 +28606,7 @@ 43: Failed Expression: atom_pin 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28603,7 +28615,7 @@ 43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28612,11 +28624,11 @@ 43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 43: **** 43: -43: [10:21:02] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [10:21:02] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [10:21:02] WARNING: not removing hydrogen atom without neighbors -43: [10:21:02] Explicit valence for atom # 1 F greater than permitted -43: [10:21:02] +43: [18:20:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [18:20:34] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [18:20:34] WARNING: not removing hydrogen atom without neighbors +43: [18:20:34] Explicit valence for atom # 1 F greater than permitted +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28625,7 +28637,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28634,7 +28646,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28643,7 +28655,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [10:21:02] +43: [18:20:34] 43: 43: **** 43: Pre-condition Violation @@ -28652,20 +28664,20 @@ 43: Failed Expression: 0 43: **** 43: -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [10:21:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [10:21:02] Unusual charge on atom 0 number of radical electrons set to zero -43: [10:21:02] Unusual charge on atom 0 number of radical electrons set to zero -43: [10:21:02] Unusual charge on atom 0 number of radical electrons set to zero -43: [10:21:02] non-ring atom 0 marked aromatic -43: [10:21:02] non-ring atom 0 marked aromatic +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [18:20:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [18:20:34] Unusual charge on atom 0 number of radical electrons set to zero +43: [18:20:34] Unusual charge on atom 0 number of radical electrons set to zero +43: [18:20:34] Unusual charge on atom 0 number of radical electrons set to zero +43: [18:20:34] non-ring atom 0 marked aromatic +43: [18:20:34] non-ring atom 0 marked aromatic 43: =============================================================================== 43: All tests passed (1316 assertions in 75 test cases) 43: - 41/208 Test #43: graphmolTestsCatch ..................... Passed 0.19 sec + 40/208 Test #43: graphmolTestsCatch ..................... Passed 0.54 sec test 44 Start 44: graphmolSGroupCatch @@ -28675,7 +28687,7 @@ 44: =============================================================================== 44: All tests passed (120 assertions in 6 test cases) 44: - 42/208 Test #44: graphmolSGroupCatch .................... Passed 0.09 sec + 41/208 Test #44: graphmolSGroupCatch .................... Passed 0.26 sec test 45 Start 45: graphmolAdjustQueryCatch @@ -28685,26 +28697,26 @@ 45: =============================================================================== 45: All tests passed (281 assertions in 10 test cases) 45: - 43/208 Test #45: graphmolAdjustQueryCatch ............... Passed 0.19 sec + 42/208 Test #45: graphmolAdjustQueryCatch ............... Passed 0.64 sec test 46 Start 46: chiralityTestsCatch 46: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/chiralityTestsCatch 46: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol 46: Test timeout computed to be: 1500 -46: [10:21:03] unable to set wavy bonds for double bonds: 3 -46: [10:21:03] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [10:21:03] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [10:21:03] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [10:21:03] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [10:21:03] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [10:21:03] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [10:21:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -46: [10:21:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +46: [18:20:35] unable to set wavy bonds for double bonds: 3 +46: [18:20:35] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [18:20:35] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [18:20:35] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [18:20:35] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [18:20:35] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [18:20:35] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [18:20:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +46: [18:20:36] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 46: =============================================================================== 46: All tests passed (1587 assertions in 50 test cases) 46: - 44/208 Test #46: chiralityTestsCatch .................... Passed 0.25 sec + 43/208 Test #46: chiralityTestsCatch .................... Passed 0.84 sec test 47 Start 47: canonTestsCatch @@ -28718,7 +28730,7 @@ 47: =============================================================================== 47: All tests passed (47 assertions in 2 test cases) 47: - 45/208 Test #47: canonTestsCatch ........................ Passed 0.10 sec + 44/208 Test #47: canonTestsCatch ........................ Passed 0.19 sec test 48 Start 48: moliteratorTestsCatch @@ -28728,15 +28740,15 @@ 48: =============================================================================== 48: All tests passed (8 assertions in 3 test cases) 48: - 46/208 Test #48: moliteratorTestsCatch .................. Passed 0.08 sec + 45/208 Test #48: moliteratorTestsCatch .................. Passed 0.17 sec test 49 Start 49: testDepictor 49: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/testDepictor 49: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor 49: Test timeout computed to be: 1500 -49: [10:21:04] Warning: stereochemistry around double bond may be incorrect in depiction. - 47/208 Test #49: testDepictor ........................... Passed 1.19 sec +49: [18:20:39] Warning: stereochemistry around double bond may be incorrect in depiction. + 46/208 Test #49: testDepictor ........................... Passed 3.36 sec test 50 Start 50: depictorCatch @@ -28746,13 +28758,17 @@ 50: =============================================================================== 50: All tests passed (65 assertions in 4 test cases) 50: - 48/208 Test #50: depictorCatch .......................... Passed 0.07 sec + 47/208 Test #50: depictorCatch .......................... Passed 0.14 sec test 51 Start 51: pyDepictor 51: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" 51: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap 51: Test timeout computed to be: 1500 +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 51: ....E..... 51: ====================================================================== 51: ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) @@ -28772,10 +28788,10 @@ 51: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 51: 51: ---------------------------------------------------------------------- -51: Ran 10 tests in 0.702s +51: Ran 10 tests in 2.047s 51: 51: FAILED (errors=1) - 49/208 Test #51: pyDepictor .............................***Failed 1.62 sec + 48/208 Test #51: pyDepictor .............................***Failed 4.33 sec ....E..... ====================================================================== ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) @@ -28795,7 +28811,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 10 tests in 0.702s +Ran 10 tests in 2.047s FAILED (errors=1) @@ -28805,24 +28821,24 @@ 52: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/smiTest1 52: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 52: Test timeout computed to be: 1500 -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] WARNING: not removing hydrogen atom without neighbors -52: [10:21:06] Invalid chiral specification on atom 0 -52: [10:21:06] Invalid chiral specification on atom 0 -52: [10:21:06] Invalid chiral specification on atom 0 -52: [10:21:06] Invalid chiral specification on atom 0 -52: [10:21:06] Invalid chiral specification on atom 0 -52: [10:21:06] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -52: [10:21:06] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] WARNING: not removing hydrogen atom without neighbors +52: [18:20:44] Invalid chiral specification on atom 0 +52: [18:20:44] Invalid chiral specification on atom 0 +52: [18:20:44] Invalid chiral specification on atom 0 +52: [18:20:44] Invalid chiral specification on atom 0 +52: [18:20:44] Invalid chiral specification on atom 0 +52: [18:20:44] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +52: [18:20:44] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 52: --C1CCC2(CC1)CCCCC2CCC1CCCC1 52: smi: ClC1CCCCC1 52: smi: ClC1CCCCC1 @@ -28837,113 +28853,113 @@ 52: CbC(bC)aC 52: O.C 52: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -52: [10:21:07] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -52: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -52: [10:21:07] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -52: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -52: [10:21:07] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -52: [10:21:07] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -52: [10:21:07] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [10:21:07] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [10:21:07] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [10:21:07] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [10:21:07] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [10:21:07] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [18:20:46] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +52: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +52: [18:20:46] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +52: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +52: [18:20:46] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +52: [18:20:46] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +52: [18:20:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [18:20:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [18:20:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [18:20:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [18:20:46] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [18:20:46] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 52: C=c1s/c2n(c1=O)CCCCCCC\N=2 52: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -52: [10:21:07] SMILES Parse Error: extra close parentheses while parsing: C) -52: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 50/208 Test #52: smiTest1 ............................... Passed 0.75 sec +52: [18:20:46] SMILES Parse Error: extra close parentheses while parsing: C) +52: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 49/208 Test #52: smiTest1 ............................... Passed 2.01 sec test 53 Start 53: smiTest2 53: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/smiTest2 53: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 53: Test timeout computed to be: 1500 -53: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -53: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -53: [10:21:07] SMILES Parse Error: syntax error while parsing: - -53: [10:21:07] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -53: [10:21:07] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -53: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -53: [10:21:07] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -53: [10:21:07] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -53: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -53: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -53: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -53: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -53: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -53: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -53: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 51/208 Test #53: smiTest2 ............................... Passed 0.04 sec +53: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +53: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +53: [18:20:46] SMILES Parse Error: syntax error while parsing: - +53: [18:20:46] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +53: [18:20:46] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +53: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +53: [18:20:46] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +53: [18:20:46] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +53: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +53: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +53: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +53: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +53: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +53: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +53: [18:20:46] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 50/208 Test #53: smiTest2 ............................... Passed 0.09 sec test 54 Start 54: cxsmilesTest 54: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/cxsmilesTest 54: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 54: Test timeout computed to be: 1500 - 52/208 Test #54: cxsmilesTest ........................... Passed 0.09 sec + 51/208 Test #54: cxsmilesTest ........................... Passed 0.18 sec test 55 Start 55: smaTest1 55: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/smaTest1 55: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 55: Test timeout computed to be: 1500 -55: [10:21:07] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -55: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -55: [10:21:07] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -55: [10:21:07] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -55: [10:21:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -55: [10:21:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 53/208 Test #55: smaTest1 ............................... Passed 0.64 sec +55: [18:20:47] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +55: [18:20:47] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +55: [18:20:47] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +55: [18:20:47] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +55: [18:20:47] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +55: [18:20:47] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 52/208 Test #55: smaTest1 ............................... Passed 1.11 sec test 56 Start 56: smiTestCatch 56: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/smiTestCatch 56: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 56: Test timeout computed to be: 1500 -56: [10:21:08] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -56: [10:21:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -56: [10:21:08] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -56: [10:21:08] SMARTS Parse Error: unclosed ring for input: 'C1C' -56: [10:21:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -56: [10:21:08] SMARTS Parse Error: syntax error while parsing: C)foo -56: [10:21:08] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -56: [10:21:08] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -56: [10:21:08] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -56: [10:21:08] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -56: [10:21:08] w block attempts to set wedging on bond 0 more than once. -56: [10:21:08] improperly formatted w block -56: [10:21:08] atom 3 is not associated with bond 1 in w block +56: [18:20:48] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +56: [18:20:48] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +56: [18:20:48] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +56: [18:20:48] SMARTS Parse Error: unclosed ring for input: 'C1C' +56: [18:20:48] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +56: [18:20:48] SMARTS Parse Error: syntax error while parsing: C)foo +56: [18:20:48] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +56: [18:20:48] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +56: [18:20:48] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +56: [18:20:48] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +56: [18:20:48] w block attempts to set wedging on bond 0 more than once. +56: [18:20:48] improperly formatted w block +56: [18:20:48] atom 3 is not associated with bond 1 in w block 56: =============================================================================== 56: All tests passed (969 assertions in 49 test cases) 56: - 54/208 Test #56: smiTestCatch ........................... Passed 0.45 sec + 53/208 Test #56: smiTestCatch ........................... Passed 1.06 sec test 57 Start 57: nontetrahedralCatch 57: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/nontetrahedralCatch 57: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 -57: [10:21:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [10:21:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [10:21:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [10:21:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [10:21:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [10:21:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [10:21:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [10:21:08] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [10:21:08] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +57: [18:20:49] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [18:20:49] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [18:20:49] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [18:20:49] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [18:20:49] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [18:20:49] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [18:20:49] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [18:20:49] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [18:20:49] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 57: =============================================================================== 57: All tests passed (308 assertions in 9 test cases) 57: - 55/208 Test #57: nontetrahedralCatch .................... Passed 0.19 sec + 54/208 Test #57: nontetrahedralCatch .................... Passed 0.56 sec test 58 Start 58: fileParsersTest1 @@ -28952,25 +28968,114 @@ 58: Test timeout computed to be: 1500 58: *************************************** 58: *************************************** - 56/208 Test #39: resMolSupplierTest ..................... Passed 16.05 sec +58: [18:20:50] bond with order 0 found on line 7. This is not part of the MDL specification. +58: [18:20:50] unrecognized query bond type, 9, found on line 7. Using an "any" query. +58: [18:20:50] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +58: [18:20:50] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +58: [18:20:50] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:20:50] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:20:50] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:20:50] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:20:50] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:20:50] Warning: molecule is tagged as 3D, but all Z coords are zero +58: generating smiles +58: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +58: converting back +58: check isomorphism +58: [18:20:57] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [18:20:57] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [18:20:57] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [18:20:57] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [18:20:57] deprecated group abbreviation ignored on line 24 +58: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +58: [18:20:57] +58: +58: **** +58: Post-condition Violation +58: Element 'Mv' not found +58: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +58: Failed Expression: anum > -1 +58: **** +58: +58: [18:21:12] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:21:12] Warning: molecule is tagged as 3D, but all Z coords are zero +58: ---------------------------------- +58: ---------------------------------- +58: [18:21:13] +58: +58: **** +58: Pre-condition Violation +58: rlabel out of range for MDL files +58: Violation occurred on line 804 in file ./Code/GraphMol/Atom.cpp +58: Failed Expression: rlabel >= 0 && rlabel < 100 +58: **** +58: +58: [18:21:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [18:21:17] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +58: [18:21:17] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +58: [18:21:17] Empty atom list: 'M ALS 1 0 F' on line 8. +58: de_DE.UTF-8 +58: [18:21:17] ------------------------------------- +58: [18:21:17] Test multithreading Locale Switching +58: [18:21:17] Test multithreading (Done) +58: [18:21:17] ------------------------------------- +58: *************************************** +58: *************************************** +58: [18:21:17] bond with order 0 found on line 7. This is not part of the MDL specification. +58: [18:21:17] unrecognized query bond type, 9, found on line 7. Using an "any" query. +58: [18:21:18] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +58: [18:21:18] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +58: [18:21:18] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:21:18] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:21:18] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:21:18] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:21:18] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:21:18] Warning: molecule is tagged as 3D, but all Z coords are zero +58: generating smiles +58: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +58: converting back +58: check isomorphism +58: [18:21:26] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [18:21:26] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [18:21:26] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [18:21:26] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [18:21:26] deprecated group abbreviation ignored on line 24 +58: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +58: [18:21:26] +58: +58: **** +58: Post-condition Violation +58: Element 'Mv' not found +58: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +58: Failed Expression: anum > -1 +58: **** +58: +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: done +25: ------------------------------------- +25: Unit tests for all MMFF constraint terms. +25: 10.0003 +25: done +25: ------------------------------------- +25: Unit test for MMFF TorsionConstraint close to 0 degrees. +25: done +25: ------------------------------------- +25: Unit tests for copying MMFF ForceFields. +25: done +25: ------------------------------------- +25: Unit test for MMFF butane scan. +25: done + 55/208 Test #25: testMMFFForceField ..................... Passed 174.51 sec test 59 Start 59: testMolSupplier 59: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testMolSupplier 59: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 59: Test timeout computed to be: 1500 -59: [10:21:08] +59: [18:21:32] 59: ----------------------------------------- -58: [10:21:08] bond with order 0 found on line 7. This is not part of the MDL specification. -58: [10:21:08] unrecognized query bond type, 9, found on line 7. Using an "any" query. -58: [10:21:08] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -58: [10:21:08] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -58: [10:21:08] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:08] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:08] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:08] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:08] Warning: molecule is tagged as 3D, but all Z coords are zero -59: [10:21:08] +59: [18:21:32] 59: 59: **** 59: Invariant Violation @@ -28979,224 +29084,219 @@ 59: Failed Expression: nSwaps < 2 59: **** 59: -58: [10:21:08] Warning: molecule is tagged as 3D, but all Z coords are zero -58: generating smiles -58: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -58: converting back -58: check isomorphism -59: [10:21:09] Finished: testMolSup() -59: [10:21:09] ----------------------------------------- +59: [18:21:33] Finished: testMolSup() +59: [18:21:33] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testRandMolSup() -59: [10:21:09] ----------------------------------------- +59: [18:21:33] ----------------------------------------- +59: [18:21:33] Finished: testRandMolSup() +59: [18:21:33] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testSmilesSup() -59: [10:21:09] ----------------------------------------- +59: [18:21:33] ----------------------------------------- +59: [18:21:33] Finished: testSmilesSup() +59: [18:21:33] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] ------------------------------------------------------ -59: [10:21:09] SMILES Parse Error: syntax error while parsing: fail -59: [10:21:09] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -59: [10:21:09] ERROR: Smiles parse error on line 3 -59: [10:21:09] ERROR: Cannot create molecule from : 'fail' -59: [10:21:09] ------------------------------------------------------ -59: [10:21:09] ------------------------------------------------------ -59: [10:21:09] >>> This may result in an infinite loop. It should finish almost immediately: -59: [10:21:09] <<< done. -59: [10:21:09] Finished: testSmilesSupFromText() -59: [10:21:09] ----------------------------------------- +59: [18:21:33] ----------------------------------------- +59: [18:21:33] ------------------------------------------------------ +59: [18:21:33] SMILES Parse Error: syntax error while parsing: fail +59: [18:21:33] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +59: [18:21:33] ERROR: Smiles parse error on line 3 +59: [18:21:33] ERROR: Cannot create molecule from : 'fail' +59: [18:21:33] ------------------------------------------------------ +59: [18:21:33] ------------------------------------------------------ +59: [18:21:33] >>> This may result in an infinite loop. It should finish almost immediately: +59: [18:21:33] <<< done. +59: [18:21:33] Finished: testSmilesSupFromText() +59: [18:21:33] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testSmilesWriter() -59: [10:21:09] ----------------------------------------- +59: [18:21:33] ----------------------------------------- +59: [18:21:33] Finished: testSmilesWriter() +59: [18:21:33] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testSDWriter() -59: [10:21:09] ----------------------------------------- +59: [18:21:33] ----------------------------------------- +59: [18:21:33] Finished: testSDWriter() +59: [18:21:33] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testSDSupplierEnding() -59: [10:21:09] ----------------------------------------- +59: [18:21:33] ----------------------------------------- +59: [18:21:33] Finished: testSDSupplierEnding() +59: [18:21:33] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testSuppliersEmptyFile() -59: [10:21:09] ----------------------------------------- +59: [18:21:33] ----------------------------------------- +59: [18:21:34] Finished: testSuppliersEmptyFile() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testCisTrans() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testCisTrans() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testStereoRound() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testStereoRound() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testIssue226() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testIssue226() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testTDTSupplier1() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testTDTSupplier1() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testTDTSupplier2() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testTDTSupplier2() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testTDTSupplier3() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testTDTSupplier3() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testSDSupplierFromText() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testSDSupplierFromText() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] ERROR: Problems encountered parsing data fields -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] ERROR: Problems encountered parsing data fields -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Spurious data before the first property will be ignored -59: [10:21:09] Property will be truncated after the first blank line -59: [10:21:09] Property will be truncated after the first blank line -59: [10:21:09] Property will be truncated after the first blank line -59: [10:21:09] Finished: testSDSupplierStrLax1() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] ERROR: Problems encountered parsing data fields +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] ERROR: Problems encountered parsing data fields +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Spurious data before the first property will be ignored +59: [18:21:34] Property will be truncated after the first blank line +59: [18:21:34] Property will be truncated after the first blank line +59: [18:21:34] Property will be truncated after the first blank line +59: [18:21:34] Finished: testSDSupplierStrLax1() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] ERROR: Problems encountered parsing data fields -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Property will be truncated after the first blank line -59: [10:21:09] Finished: testSDSupplierStrLax2() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] ERROR: Problems encountered parsing data fields +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Property will be truncated after the first blank line +59: [18:21:34] Finished: testSDSupplierStrLax2() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] ERROR: Problems encountered parsing data fields -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] ERROR: Problems encountered parsing data fields -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Spurious data before the first property will be ignored -59: [10:21:09] Property will be truncated after the first blank line -59: [10:21:09] Property will be truncated after the first blank line -59: [10:21:09] Property will be truncated after the first blank line -59: [10:21:09] Finished: testSDSupplierFromTextStrLax1() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] ERROR: Problems encountered parsing data fields +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] ERROR: Problems encountered parsing data fields +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Spurious data before the first property will be ignored +59: [18:21:34] Property will be truncated after the first blank line +59: [18:21:34] Property will be truncated after the first blank line +59: [18:21:34] Property will be truncated after the first blank line +59: [18:21:34] Finished: testSDSupplierFromTextStrLax1() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] ERROR: Problems encountered parsing data fields -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Property will be truncated after the first blank line -59: [10:21:09] Finished: testSDSupplierFromTextStrLax2() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] ERROR: Problems encountered parsing data fields +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Property will be truncated after the first blank line +59: [18:21:34] Finished: testSDSupplierFromTextStrLax2() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testIssue265() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testIssue265() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] ERROR: End of data field name not found -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Explicit valence for atom # 0 F, 2, is greater than permitted -59: [10:21:09] ERROR: Could not sanitize molecule ending on line 16 -59: [10:21:09] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -59: [10:21:09] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] ERROR: Bond line too short: 'M END' on line 18 -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Finished: testSDErrorHandling() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] ERROR: End of data field name not found +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Explicit valence for atom # 0 F, 2, is greater than permitted +59: [18:21:34] ERROR: Could not sanitize molecule ending on line 16 +59: [18:21:34] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +59: [18:21:34] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] ERROR: Bond line too short: 'M END' on line 18 +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Finished: testSDErrorHandling() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testIssue381() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testIssue381() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testSetStreamIndices() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testSetStreamIndices() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testMixIterAndRandom() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testMixIterAndRandom() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- 59: build: -59: [10:21:09] Finished: testRemoveHs() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] Finished: testRemoveHs() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testGetItemText() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testGetItemText() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testForwardSDSupplier() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testForwardSDSupplier() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testMissingCRSDSupplier() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testMissingCRSDSupplier() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testIssue3482695() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testIssue3482695() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] ERROR: Cannot convert 'foo' to unsigned int on line 557 -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Finished: testIssue3525673() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] ERROR: Cannot convert 'foo' to unsigned int on line 557 +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Finished: testIssue3525673() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testBlankLinesInProps() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testBlankLinesInProps() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testSkipLines() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testSkipLines() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testGitHub23() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testGitHub23() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testGitHub88() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testGitHub88() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testGitHub2285() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testGitHub2285() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -59: [10:21:09] ERROR: Smiles parse error on line 1 -59: [10:21:09] ERROR: Cannot create molecule from : 'c1ccccc' -59: [10:21:09] SMILES Parse Error: extra open parentheses for input: 'C(C' -59: [10:21:09] ERROR: Smiles parse error on line 3 -59: [10:21:09] ERROR: Cannot create molecule from : 'C(C' -59: [10:21:09] Explicit valence for atom # 1 C, 5, is greater than permitted -59: [10:21:09] ERROR: Could not sanitize molecule on line 5 -59: [10:21:09] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -59: [10:21:09] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [10:21:09] ERROR: Could not sanitize molecule ending on line 21 -59: [10:21:09] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [10:21:09] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [10:21:09] ERROR: Could not sanitize molecule ending on line 21 -59: [10:21:09] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [10:21:09] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [10:21:09] ERROR: Could not sanitize molecule ending on line 21 -59: [10:21:09] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [10:21:09] ERROR: Atom line too short: ' -9.6' on line 28 -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [10:21:09] ERROR: Could not sanitize molecule ending on line 21 -59: [10:21:09] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [10:21:09] ERROR: Atom line too short: ' -9.6' on line 28 -59: [10:21:09] ERROR: moving to the beginning of the next molecule -59: [10:21:09] Finished: testGitHub2479() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +59: [18:21:34] ERROR: Smiles parse error on line 1 +59: [18:21:34] ERROR: Cannot create molecule from : 'c1ccccc' +59: [18:21:34] SMILES Parse Error: extra open parentheses for input: 'C(C' +59: [18:21:34] ERROR: Smiles parse error on line 3 +59: [18:21:34] ERROR: Cannot create molecule from : 'C(C' +59: [18:21:34] Explicit valence for atom # 1 C, 5, is greater than permitted +59: [18:21:34] ERROR: Could not sanitize molecule on line 5 +59: [18:21:34] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +59: [18:21:34] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [18:21:34] ERROR: Could not sanitize molecule ending on line 21 +59: [18:21:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [18:21:34] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [18:21:34] ERROR: Could not sanitize molecule ending on line 21 +59: [18:21:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [18:21:34] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [18:21:34] ERROR: Could not sanitize molecule ending on line 21 +59: [18:21:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [18:21:34] ERROR: Atom line too short: ' -9.6' on line 28 +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [18:21:34] ERROR: Could not sanitize molecule ending on line 21 +59: [18:21:34] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [18:21:34] ERROR: Atom line too short: ' -9.6' on line 28 +59: [18:21:34] ERROR: moving to the beginning of the next molecule +59: [18:21:34] Finished: testGitHub2479() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] +59: [18:21:34] ----------------------------------------- +59: [18:21:34] 59: 59: **** 59: Invariant Violation @@ -29205,74 +29305,59 @@ 59: Failed Expression: bnd 59: **** 59: -59: [10:21:09] Finished: testGitHub2881() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] Finished: testGitHub2881() +59: [18:21:34] ----------------------------------------- 59: -59: [10:21:09] ----------------------------------------- -59: [10:21:09] Finished: testGitHub3517() -59: [10:21:09] ----------------------------------------- +59: [18:21:34] ----------------------------------------- +59: [18:21:34] Finished: testGitHub3517() +59: [18:21:34] ----------------------------------------- 59: - 57/208 Test #59: testMolSupplier ........................ Passed 1.12 sec + 56/208 Test #59: testMolSupplier ........................ Passed 2.10 sec test 60 Start 60: testGeneralFileReader 60: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testGeneralFileReader 60: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 60: Test timeout computed to be: 1500 -60: [10:21:09] +60: [18:21:34] 60: ----------------------------------------- -60: [10:21:09] Finished: testDetermineFormat() -60: [10:21:09] ----------------------------------------- +60: [18:21:34] Finished: testDetermineFormat() +60: [18:21:34] ----------------------------------------- 60: -60: [10:21:09] +60: [18:21:34] 60: ----------------------------------------- -60: [10:21:10] Finished: testSdf() -60: [10:21:10] ----------------------------------------- +60: [18:21:34] Finished: testSdf() +60: [18:21:34] ----------------------------------------- 60: -60: [10:21:10] +60: [18:21:34] 60: ----------------------------------------- -60: [10:21:10] Finished: testSmi() -60: [10:21:10] ----------------------------------------- +60: [18:21:34] Finished: testSmi() +60: [18:21:34] ----------------------------------------- 60: -60: [10:21:10] +60: [18:21:34] 60: ----------------------------------------- -60: [10:21:10] Finished: testMae() -60: [10:21:10] ----------------------------------------- +60: [18:21:35] Finished: testMae() +60: [18:21:35] ----------------------------------------- 60: -60: [10:21:10] +60: [18:21:35] 60: ----------------------------------------- -60: [10:21:10] Finished: testTdt() -60: [10:21:10] ----------------------------------------- +60: [18:21:35] Finished: testTdt() +60: [18:21:35] ----------------------------------------- 60: - 58/208 Test #60: testGeneralFileReader .................. Passed 0.41 sec + 57/208 Test #60: testGeneralFileReader .................. Passed 1.04 sec test 61 Start 61: testMultithreadedMolSupplier 61: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 61: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 61: Test timeout computed to be: 1500 -61: [10:21:10] +61: [18:21:35] 61: ----------------------------------------- -58: [10:21:13] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [10:21:13] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [10:21:13] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [10:21:13] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [10:21:13] deprecated group abbreviation ignored on line 24 -58: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -58: [10:21:13] -58: -58: **** -58: Post-condition Violation -58: Element 'Mv' not found -58: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -58: Failed Expression: anum > -1 -58: **** -58: -58: [10:21:26] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:26] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:21:43] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [18:21:43] Warning: molecule is tagged as 3D, but all Z coords are zero 58: ---------------------------------- 58: ---------------------------------- -58: [10:21:26] +58: [18:21:45] 58: 58: **** 58: Pre-condition Violation @@ -29281,70 +29366,37 @@ 58: Failed Expression: rlabel >= 0 && rlabel < 100 58: **** 58: -58: [10:21:26] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [10:21:28] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -58: [10:21:28] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -58: [10:21:28] Empty atom list: 'M ALS 1 0 F' on line 8. -58: de_DE.UTF-8 -58: [10:21:28] ------------------------------------- -58: [10:21:28] Test multithreading Locale Switching -61: [10:21:28] Finished: testSmiCorrectness() -61: [10:21:28] ----------------------------------------- -61: -61: [10:21:28] -61: ----------------------------------------- -61: [10:21:28] Spurious data before the first property will be ignored -61: [10:21:28] Property will be truncated after the first blank line -61: [10:21:28] Property will be truncated after the first blank line -61: [10:21:28] Property will be truncated after the first blank line -58: [10:21:28] Test multithreading (Done) -58: [10:21:28] ------------------------------------- -58: *************************************** -58: *************************************** -58: [10:21:28] bond with order 0 found on line 7. This is not part of the MDL specification. -58: [10:21:28] unrecognized query bond type, 9, found on line 7. Using an "any" query. -58: [10:21:28] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -58: [10:21:28] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -58: [10:21:28] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:28] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:28] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:28] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:28] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:28] Warning: molecule is tagged as 3D, but all Z coords are zero -58: generating smiles -58: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -58: converting back -58: check isomorphism -61: [10:21:29] Finished: testSDCorrectness() -61: [10:21:29] ----------------------------------------- -61: - 59/208 Test #61: testMultithreadedMolSupplier ........... Passed 19.63 sec +58: [18:21:45] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [18:21:48] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +58: [18:21:48] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +58: [18:21:49] Empty atom list: 'M ALS 1 0 F' on line 8. + 58/208 Test #58: fileParsersTest1 ....................... Passed 59.65 sec test 62 Start 62: testMolWriter 62: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testMolWriter 62: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 62: Test timeout computed to be: 1500 -62: [10:21:30] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [10:21:30] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [10:21:30] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [10:21:30] bond with order 0 found on line 11. This is not part of the MDL specification. -62: [10:21:30] bond with order 0 found on line 16. This is not part of the MDL specification. - 60/208 Test #62: testMolWriter .......................... Passed 1.02 sec +62: [18:21:51] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [18:21:51] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [18:21:51] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [18:21:51] bond with order 0 found on line 11. This is not part of the MDL specification. +62: [18:21:51] bond with order 0 found on line 16. This is not part of the MDL specification. + 59/208 Test #62: testMolWriter .......................... Passed 3.00 sec test 63 Start 63: testTplParser 63: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testTplParser 63: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 63: Test timeout computed to be: 1500 - 61/208 Test #63: testTplParser .......................... Passed 0.10 sec + 60/208 Test #63: testTplParser .......................... Passed 0.37 sec test 64 Start 64: testMol2ToMol 64: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testMol2ToMol 64: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 64: Test timeout computed to be: 1500 - 62/208 Test #64: testMol2ToMol .......................... Passed 0.13 sec + 61/208 Test #64: testMol2ToMol .......................... Passed 0.52 sec test 65 Start 65: testSequence @@ -30335,39 +30387,39 @@ 65: CONECT 27 28 28 29 65: END 65: - 63/208 Test #65: testSequence ........................... Passed 0.24 sec + 62/208 Test #65: testSequence ........................... Passed 0.29 sec test 66 Start 66: testExtendedStereoParsing 66: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testExtendedStereoParsing 66: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 66: Test timeout computed to be: 1500 - 64/208 Test #66: testExtendedStereoParsing .............. Passed 0.09 sec + 63/208 Test #66: testExtendedStereoParsing .............. Passed 0.30 sec test 67 Start 67: fileParsersCatchTest 67: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/fileParsersCatchTest 67: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 -67: [10:21:31] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -67: [10:21:31] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -67: [10:21:31] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [10:21:31] SGroup 1 is invalid and will be ignored -67: [10:21:31] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -67: [10:21:31] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [10:21:31] SGroup 1 is invalid and will be ignored -67: [10:21:31] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -67: [10:21:31] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -67: [10:21:31] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -67: [10:21:31] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -67: [10:21:31] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [10:21:31] SGroup 1 is invalid and will be ignored -67: [10:21:31] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -67: [10:21:31] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -67: [10:21:31] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [10:21:31] SGroup 1 is invalid and will be ignored -67: [10:21:31] SGroup 3 referenced on line 40 not found. -67: [10:21:31] +67: [18:21:53] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +67: [18:21:53] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +67: [18:21:53] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [18:21:53] SGroup 1 is invalid and will be ignored +67: [18:21:53] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +67: [18:21:53] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [18:21:53] SGroup 1 is invalid and will be ignored +67: [18:21:53] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +67: [18:21:53] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +67: [18:21:53] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +67: [18:21:53] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +67: [18:21:53] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [18:21:53] SGroup 1 is invalid and will be ignored +67: [18:21:53] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +67: [18:21:53] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +67: [18:21:53] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [18:21:53] SGroup 1 is invalid and will be ignored +67: [18:21:53] SGroup 3 referenced on line 40 not found. +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30376,8 +30428,8 @@ 67: Failed Expression: !d_bonds.empty() 67: **** 67: -67: [10:21:31] SGroup 3 referenced on line 40 not found. -67: [10:21:31] +67: [18:21:53] SGroup 3 referenced on line 40 not found. +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30386,13 +30438,13 @@ 67: Failed Expression: !d_bonds.empty() 67: **** 67: -67: [10:21:31] no bonds -67: [10:21:31] SGroup 1 is invalid and will be ignored -67: [10:21:31] SGroup line too short: 'M SBV 1 6' on line 42 -67: [10:21:31] SGroup 1 is invalid and will be ignored -67: [10:21:31] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -67: [10:21:31] SGroup 2 is invalid and will be ignored -67: [10:21:31] +67: [18:21:53] no bonds +67: [18:21:53] SGroup 1 is invalid and will be ignored +67: [18:21:53] SGroup line too short: 'M SBV 1 6' on line 42 +67: [18:21:53] SGroup 1 is invalid and will be ignored +67: [18:21:53] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +67: [18:21:53] SGroup 2 is invalid and will be ignored +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30401,7 +30453,7 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30410,8 +30462,8 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] multiple bonds with same bookmark -67: [10:21:31] +67: [18:21:53] multiple bonds with same bookmark +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30420,9 +30472,9 @@ 67: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 67: **** 67: -67: [10:21:31] bond is not part of the SubstanceGroup -67: [10:21:31] SGroup 2 is invalid and will be ignored -67: [10:21:31] +67: [18:21:53] bond is not part of the SubstanceGroup +67: [18:21:53] SGroup 2 is invalid and will be ignored +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30431,7 +30483,7 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30440,11 +30492,11 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] multiple atoms with same bookmark -67: [10:21:31] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -67: [10:21:31] SGroup 2 is invalid and will be ignored -67: [10:21:31] WARNING: final character of V3000 array is not ')' -67: [10:21:31] +67: [18:21:53] multiple atoms with same bookmark +67: [18:21:53] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +67: [18:21:53] SGroup 2 is invalid and will be ignored +67: [18:21:53] WARNING: final character of V3000 array is not ')' +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30453,8 +30505,8 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] WARNING: final character of V3000 array is not ')' -67: [10:21:31] +67: [18:21:53] WARNING: final character of V3000 array is not ')' +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30463,10 +30515,10 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] multiple bonds with same bookmark -67: [10:21:31] SGroup 1 is invalid and will be ignored -67: [10:21:31] WARNING: final character of V3000 array is not ')' -67: [10:21:31] +67: [18:21:53] multiple bonds with same bookmark +67: [18:21:53] SGroup 1 is invalid and will be ignored +67: [18:21:53] WARNING: final character of V3000 array is not ')' +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30475,8 +30527,8 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] WARNING: final character of V3000 array is not ')' -67: [10:21:31] +67: [18:21:53] WARNING: final character of V3000 array is not ')' +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30485,9 +30537,9 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] multiple atoms with same bookmark -67: [10:21:31] SGroup 1 is invalid and will be ignored -67: [10:21:31] +67: [18:21:53] multiple atoms with same bookmark +67: [18:21:53] SGroup 1 is invalid and will be ignored +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30496,7 +30548,7 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30505,9 +30557,9 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] multiple bonds with same bookmark -67: [10:21:31] SGroup 2 is invalid and will be ignored -67: [10:21:31] +67: [18:21:53] multiple bonds with same bookmark +67: [18:21:53] SGroup 2 is invalid and will be ignored +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30516,7 +30568,7 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] +67: [18:21:53] 67: 67: **** 67: Pre-condition Violation @@ -30525,14 +30577,14 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [10:21:31] multiple atoms with same bookmark -67: [10:21:31] SGroup 2 is invalid and will be ignored -67: [10:21:31] Explicit valence for atom # 2 O, 3, is greater than permitted -67: [10:21:31] Explicit valence for atom # 1 O, 3, is greater than permitted -67: [10:21:31] Explicit valence for atom # 1 C, 5, is greater than permitted -67: [10:21:31] sanitise [10:21:31] UNK: [10:21:31] Warning: molecule is tagged as 3D, but all Z coords are zero -67: [10:21:31] skipping block at line 7: 'BEGIN ATOM' -67: [10:21:31] +67: [18:21:53] multiple atoms with same bookmark +67: [18:21:53] SGroup 2 is invalid and will be ignored +67: [18:21:53] Explicit valence for atom # 2 O, 3, is greater than permitted +67: [18:21:53] Explicit valence for atom # 1 O, 3, is greater than permitted +67: [18:21:53] Explicit valence for atom # 1 C, 5, is greater than permitted +67: [18:21:53] sanitise [18:21:53] UNK: [18:21:54] Warning: molecule is tagged as 3D, but all Z coords are zero +67: [18:21:54] skipping block at line 7: 'BEGIN ATOM' +67: [18:21:54] 67: 67: **** 67: Pre-condition Violation @@ -30541,7 +30593,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [10:21:31] +67: [18:21:54] 67: 67: **** 67: Pre-condition Violation @@ -30550,7 +30602,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [10:21:31] +67: [18:21:54] 67: 67: **** 67: Pre-condition Violation @@ -30559,7 +30611,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [10:21:31] +67: [18:21:54] 67: 67: **** 67: Pre-condition Violation @@ -30568,7 +30620,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [10:21:31] +67: [18:21:54] 67: 67: **** 67: Pre-condition Violation @@ -30577,9 +30629,9 @@ 67: Failed Expression: dp_sInStream != nullptr 67: **** 67: -67: [10:21:31] Found a SCD/SED line with missing/empty SDT specification at line 21 -67: [10:21:31] Found a SCD/SED line with missing/empty SDT specification at line 20 -67: [10:21:31] +67: [18:21:54] Found a SCD/SED line with missing/empty SDT specification at line 21 +67: [18:21:54] Found a SCD/SED line with missing/empty SDT specification at line 20 +67: [18:21:54] 67: 67: **** 67: Post-condition Violation @@ -30588,13 +30640,13 @@ 67: Failed Expression: anum > -1 67: **** 67: -67: [10:21:31] BEGIN SGROUP line not found on line 14 -67: [10:21:31] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -67: [10:21:31] END SGROUP line not found on line 14 -67: [10:21:31] END SGROUP line not found on line 14 -67: [10:21:31] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -67: [10:21:31] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -67: [10:21:31] +67: [18:21:54] BEGIN SGROUP line not found on line 14 +67: [18:21:54] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +67: [18:21:54] END SGROUP line not found on line 14 +67: [18:21:54] END SGROUP line not found on line 14 +67: [18:21:54] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +67: [18:21:54] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +67: [18:21:54] 67: 67: **** 67: Range Error @@ -30603,21 +30655,21 @@ 67: Failed Expression: 99 < 9 67: **** 67: -67: [10:21:31] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -67: [10:21:31] Multiple ATTCHPT values for atom 2 on line 9 -67: [10:21:31] Found a SCD/SED line with missing/empty SDT specification at line 12 -67: [10:21:31] SMARTS Parse Error: syntax error while parsing: [#6;R -67: [10:21:31] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -67: [10:21:31] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -67: [10:21:31] Skipping empty SMARTS value for SMARTSQ. -67: [10:21:31] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -67: [10:21:31] Found a SCD/SED line with missing/empty SDT specification at line 12 -67: [10:21:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -67: [10:21:31] Warning: molecule is tagged as 3D, but all Z coords are zero +67: [18:21:54] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +67: [18:21:54] Multiple ATTCHPT values for atom 2 on line 9 +67: [18:21:54] Found a SCD/SED line with missing/empty SDT specification at line 12 +67: [18:21:54] SMARTS Parse Error: syntax error while parsing: [#6;R +67: [18:21:54] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +67: [18:21:54] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +67: [18:21:54] Skipping empty SMARTS value for SMARTSQ. +67: [18:21:54] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +67: [18:21:54] Found a SCD/SED line with missing/empty SDT specification at line 12 +67: [18:21:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +67: [18:21:54] Warning: molecule is tagged as 3D, but all Z coords are zero 67: =============================================================================== 67: All tests passed (778 assertions in 67 test cases) 67: - 65/208 Test #67: fileParsersCatchTest ................... Passed 0.38 sec + 64/208 Test #67: fileParsersCatchTest ................... Passed 0.81 sec test 68 Start 68: testPropertyLists @@ -30627,7 +30679,7 @@ 68: =============================================================================== 68: All tests passed (94 assertions in 4 test cases) 68: - 66/208 Test #68: testPropertyLists ...................... Passed 0.09 sec + 65/208 Test #68: testPropertyLists ...................... Passed 0.15 sec test 69 Start 69: XYZFileParserCatchTest @@ -30637,45 +30689,45 @@ 69: =============================================================================== 69: All tests passed (100 assertions in 2 test cases) 69: - 67/208 Test #69: XYZFileParserCatchTest ................. Passed 0.09 sec + 66/208 Test #69: XYZFileParserCatchTest ................. Passed 0.17 sec test 70 Start 70: cdxmlParserCatchTest 70: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/cdxmlParserCatchTest 70: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 -70: [10:21:32] Invalid or missing fragment id from CDXML fragment, assigning new one... -70: [10:21:32] Explicit valence for atom # 3 N, 4, is greater than permitted -70: [10:21:32] CDXMLParser: failed sanitizing skipping fragment 32 -70: [10:21:32] Bad bond in CDXML skipping fragment 58... -70: [10:21:32] Invalid or missing fragment id from CDXML fragment, assigning new one... -70: [10:21:32] Bad bond in CDXML skipping fragment 58... -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] WARNING: not removing hydrogen atom without neighbors -70: [10:21:32] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. -70: [10:21:32] Incomplete atom labelling, cannot make bond -70: [10:21:32] Incomplete atom labelling, cannot make bond -70: [10:21:32] Incomplete atom labelling, cannot make bond -70: [10:21:32] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [10:21:32] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [10:21:32] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -70: [10:21:32] Failed to parse XML fragment 5 node: b attribute: Order: 5 -70: [10:21:32] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [10:21:32] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [10:21:32] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -70: [10:21:32] Failed to parse XML fragment 5 node: b attribute: Order: 5 +70: [18:21:55] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [18:21:55] Explicit valence for atom # 3 N, 4, is greater than permitted +70: [18:21:55] CDXMLParser: failed sanitizing skipping fragment 32 +70: [18:21:55] Bad bond in CDXML skipping fragment 58... +70: [18:21:55] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [18:21:55] Bad bond in CDXML skipping fragment 58... +70: [18:21:55] WARNING: not removing hydrogen atom without neighbors +70: [18:21:55] WARNING: not removing hydrogen atom without neighbors +70: [18:21:55] WARNING: not removing hydrogen atom without neighbors +70: [18:21:55] WARNING: not removing hydrogen atom without neighbors +70: [18:21:56] WARNING: not removing hydrogen atom without neighbors +70: [18:21:56] WARNING: not removing hydrogen atom without neighbors +70: [18:21:56] WARNING: not removing hydrogen atom without neighbors +70: [18:21:56] WARNING: not removing hydrogen atom without neighbors +70: [18:21:56] WARNING: not removing hydrogen atom without neighbors +70: [18:21:56] WARNING: not removing hydrogen atom without neighbors +70: [18:21:56] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. +70: [18:21:56] Incomplete atom labelling, cannot make bond +70: [18:21:56] Incomplete atom labelling, cannot make bond +70: [18:21:56] Incomplete atom labelling, cannot make bond +70: [18:21:56] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [18:21:56] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [18:21:56] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +70: [18:21:56] Failed to parse XML fragment 5 node: b attribute: Order: 5 +70: [18:21:56] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [18:21:56] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [18:21:56] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +70: [18:21:56] Failed to parse XML fragment 5 node: b attribute: Order: 5 70: =============================================================================== 70: All tests passed (200 assertions in 1 test case) 70: - 68/208 Test #70: cdxmlParserCatchTest ................... Passed 0.44 sec + 67/208 Test #70: cdxmlParserCatchTest ................... Passed 2.17 sec test 71 Start 71: testSubstructMatch @@ -30706,8 +30758,8 @@ 71: ----------------- Testing serial numbers on recursive queries 71: Done 71: -71: [10:21:32] ------------------------------------- -71: [10:21:32] Test multithreading +71: [18:21:57] ------------------------------------- +71: [18:21:57] Test multithreading 71: reading molecules 71: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 71: processing @@ -30715,21 +30767,6 @@ 71: launch :1 71: launch :2 71: launch :3 -58: [10:21:32] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [10:21:32] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [10:21:32] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [10:21:32] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [10:21:32] deprecated group abbreviation ignored on line 24 -58: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -58: [10:21:32] -58: -58: **** -58: Post-condition Violation -58: Element 'Mv' not found -58: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -58: Failed Expression: anum > -1 -58: **** -58: 71: done 71: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 71: processing2 @@ -30746,34 +30783,34 @@ 71: launch3 :2 71: launch3 :3 71: done -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Test GitHub issue 15 -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Test GitHub issue 409 -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Test chiral matching -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Test dative-bond matching -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Test cis/trans matching -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Test cis/trans matching part 2 -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -71: [10:21:33] done -71: [10:21:33] ------------------------------------- -71: [10:21:33] Testing matching E/Z against Cis/Trans stereo bonds -71: [10:21:33] +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Test GitHub issue 15 +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Test GitHub issue 409 +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Test chiral matching +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Test dative-bond matching +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Test cis/trans matching +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Test cis/trans matching part 2 +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +71: [18:22:00] done +71: [18:22:00] ------------------------------------- +71: [18:22:00] Testing matching E/Z against Cis/Trans stereo bonds +71: [18:22:00] 71: 71: **** 71: Pre-condition Violation @@ -30782,7 +30819,7 @@ 71: Failed Expression: !matches.empty() 71: **** 71: -71: [10:21:33] +71: [18:22:00] 71: 71: **** 71: Pre-condition Violation @@ -30791,7 +30828,7 @@ 71: Failed Expression: !matches.empty() 71: **** 71: - 69/208 Test #71: testSubstructMatch ..................... Passed 1.21 sec + 68/208 Test #71: testSubstructMatch ..................... Passed 3.58 sec test 72 Start 72: substructTestCatch @@ -30801,7 +30838,7 @@ 72: =============================================================================== 72: All tests passed (91 assertions in 5 test cases) 72: - 70/208 Test #72: substructTestCatch ..................... Passed 0.89 sec + 69/208 Test #72: substructTestCatch ..................... Passed 2.17 sec test 73 Start 73: testGenericGroups @@ -30811,7 +30848,7 @@ 73: =============================================================================== 73: All tests passed (490 assertions in 18 test cases) 73: - 71/208 Test #73: testGenericGroups ...................... Passed 0.17 sec + 70/208 Test #73: testGenericGroups ...................... Passed 0.58 sec test 74 Start 74: testReaction @@ -30821,189 +30858,189 @@ 74: smi: O=C1CNC(=O)CN1 74: 1: O=C1CNC(=O)CN1 74: 2: COOC -74: [10:21:34] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -74: [10:21:34] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +74: [18:22:03] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +74: [18:22:03] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 74: O=C1CNC(=O)CN1 -74: [10:21:34] product atom-mapping number 1 found multiple times. -74: [10:21:34] mapped atoms in the reactants were not mapped in the products. +74: [18:22:03] product atom-mapping number 1 found multiple times. +74: [18:22:03] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 4 -74: [10:21:35] atom 0 in product 0 has multiple charge specifications. +74: [18:22:03] atom 0 in product 0 has multiple charge specifications. 74: mass: 15.0001 74: Oc1ccccn1 74: Oc1ccc[nH]1 -74: [10:21:35] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -74: [10:21:35] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -74: [10:21:35] SMARTS Parse Error: syntax error while parsing: ([C:2] -74: [10:21:35] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -74: [10:21:35] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -74: [10:21:35] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -74: [10:21:35] SMARTS Parse Error: syntax error while parsing: [C:2]) -74: [10:21:35] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -74: [10:21:35] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -74: [10:21:35] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -74: [10:21:35] reactant 2 has no mapped atoms. -74: [10:21:35] >> Atoms within one molecule have different RXN roles. -74: [10:21:35] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -74: [10:21:35] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -74: [10:21:35] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -74: [10:21:35] SMARTS Parse Error: syntax error while parsing: ([C:2] -74: [10:21:35] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -74: [10:21:35] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -74: [10:21:35] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -74: [10:21:35] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -74: [10:21:35] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -74: [10:21:35] reactant 0 has no mapped atoms. -74: [10:21:35] reactant 1 has no mapped atoms. -74: [10:21:35] reactant 3 has no mapped atoms. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 5 found multiple times. -74: [10:21:35] product atom-mapping number 6 found multiple times. -74: [10:21:35] product atom-mapping number 7 found multiple times. -74: [10:21:35] product atom-mapping number 8 found multiple times. -74: [10:21:35] product atom-mapping number 12 found multiple times. -74: [10:21:35] product atom-mapping number 9 found multiple times. -74: [10:21:35] product atom-mapping number 10 found multiple times. -74: [10:21:35] product atom-mapping number 11 found multiple times. -74: [10:21:35] reactant 0 has no mapped atoms. -74: [10:21:35] reactant 1 has no mapped atoms. -74: [10:21:35] reactant 3 has no mapped atoms. -74: [10:21:35] reactant atom-mapping number 19 found multiple times. -74: [10:21:35] reactant atom-mapping number 25 found multiple times. -74: [10:21:35] reactant atom-mapping number 20 found multiple times. -74: [10:21:35] reactant atom-mapping number 21 found multiple times. -74: [10:21:35] reactant atom-mapping number 22 found multiple times. -74: [10:21:35] reactant atom-mapping number 23 found multiple times. -74: [10:21:35] reactant atom-mapping number 24 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. +74: [18:22:04] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +74: [18:22:04] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +74: [18:22:04] SMARTS Parse Error: syntax error while parsing: ([C:2] +74: [18:22:04] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +74: [18:22:04] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +74: [18:22:04] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +74: [18:22:04] SMARTS Parse Error: syntax error while parsing: [C:2]) +74: [18:22:04] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +74: [18:22:04] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +74: [18:22:04] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +74: [18:22:04] reactant 2 has no mapped atoms. +74: [18:22:04] >> Atoms within one molecule have different RXN roles. +74: [18:22:04] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +74: [18:22:04] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +74: [18:22:04] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +74: [18:22:04] SMARTS Parse Error: syntax error while parsing: ([C:2] +74: [18:22:04] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +74: [18:22:04] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +74: [18:22:04] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +74: [18:22:04] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +74: [18:22:04] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +74: [18:22:04] reactant 0 has no mapped atoms. +74: [18:22:04] reactant 1 has no mapped atoms. +74: [18:22:04] reactant 3 has no mapped atoms. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 5 found multiple times. +74: [18:22:04] product atom-mapping number 6 found multiple times. +74: [18:22:04] product atom-mapping number 7 found multiple times. +74: [18:22:04] product atom-mapping number 8 found multiple times. +74: [18:22:04] product atom-mapping number 12 found multiple times. +74: [18:22:04] product atom-mapping number 9 found multiple times. +74: [18:22:04] product atom-mapping number 10 found multiple times. +74: [18:22:04] product atom-mapping number 11 found multiple times. +74: [18:22:04] reactant 0 has no mapped atoms. +74: [18:22:04] reactant 1 has no mapped atoms. +74: [18:22:04] reactant 3 has no mapped atoms. +74: [18:22:04] reactant atom-mapping number 19 found multiple times. +74: [18:22:04] reactant atom-mapping number 25 found multiple times. +74: [18:22:04] reactant atom-mapping number 20 found multiple times. +74: [18:22:04] reactant atom-mapping number 21 found multiple times. +74: [18:22:04] reactant atom-mapping number 22 found multiple times. +74: [18:22:04] reactant atom-mapping number 23 found multiple times. +74: [18:22:04] reactant atom-mapping number 24 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. 74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. 74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [10:21:35] product atom-mapping number 5 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 5 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 5 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 5 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. 74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [10:21:35] product atom-mapping number 5 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 5 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 5 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 5 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. 74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. 74: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. 74: F[C@](Cl)(Br)O[C@](F)(Cl)Br -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 4 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] mapped atoms in the reactants were not mapped in the products. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 4 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 4 -74: [10:21:35] product atom-mapping number 3 found multiple times. -74: [10:21:35] product atom-mapping number 2 found multiple times. -74: [10:21:35] product atom-mapping number 1 found multiple times. -74: [10:21:35] mapped atoms in the reactants were not mapped in the products. +74: [18:22:04] product atom-mapping number 3 found multiple times. +74: [18:22:04] product atom-mapping number 2 found multiple times. +74: [18:22:04] product atom-mapping number 1 found multiple times. +74: [18:22:04] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 4 -74: [10:21:35] product atom-mapping number 6 not found in reactants. -74: [10:21:35] product atom-mapping number 7 not found in reactants. -74: [10:21:35] product atom-mapping number 8 not found in reactants. -74: [10:21:35] product atom-mapping number 7 not found in reactants. -74: [10:21:35] product atom-mapping number 8 not found in reactants. -74: [10:21:35] product atom-mapping number 9 not found in reactants. -74: [10:21:35] product atom-mapping number 10 not found in reactants. -74: [10:21:35] mapped atoms in the reactants were not mapped in the products. +74: [18:22:04] product atom-mapping number 6 not found in reactants. +74: [18:22:04] product atom-mapping number 7 not found in reactants. +74: [18:22:04] product atom-mapping number 8 not found in reactants. +74: [18:22:04] product atom-mapping number 7 not found in reactants. +74: [18:22:04] product atom-mapping number 8 not found in reactants. +74: [18:22:04] product atom-mapping number 9 not found in reactants. +74: [18:22:04] product atom-mapping number 10 not found in reactants. +74: [18:22:04] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 6 -74: [10:21:35] product atom-mapping number 7 not found in reactants. -74: [10:21:35] product atom-mapping number 8 not found in reactants. -74: [10:21:35] product atom-mapping number 9 not found in reactants. -74: [10:21:35] product atom-mapping number 10 not found in reactants. -74: [10:21:35] mapped atoms in the reactants were not mapped in the products. +74: [18:22:04] product atom-mapping number 7 not found in reactants. +74: [18:22:04] product atom-mapping number 8 not found in reactants. +74: [18:22:04] product atom-mapping number 9 not found in reactants. +74: [18:22:04] product atom-mapping number 10 not found in reactants. +74: [18:22:04] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 6 74: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 74: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -74: [10:21:35] mapped atoms in the reactants were not mapped in the products. +74: [18:22:04] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -74: [10:21:35] product atom-mapping number 17 not found in reactants. -74: [10:21:35] product atom-mapping number 18 not found in reactants. -74: [10:21:35] mapped atoms in the reactants were not mapped in the products. +74: [18:22:05] product atom-mapping number 17 not found in reactants. +74: [18:22:05] product atom-mapping number 18 not found in reactants. +74: [18:22:05] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 12 -74: [10:21:35] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -74: [10:21:35] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +74: [18:22:05] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +74: [18:22:05] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 74: -74: [10:21:35] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +74: [18:22:05] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 74: ------------- 74: CCOc1ccccc1 -74: [10:21:36] reactant 0 has no mapped atoms. -74: [10:21:36] product 0 has no mapped atoms. -74: [10:21:36] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. - 72/208 Test #74: testReaction ........................... Passed 1.76 sec +74: [18:22:08] reactant 0 has no mapped atoms. +74: [18:22:08] product 0 has no mapped atoms. +74: [18:22:08] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 71/208 Test #74: testReaction ........................... Passed 5.72 sec test 75 Start 75: testReactionFingerprints 75: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/testReactionFingerprints 75: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions 75: Test timeout computed to be: 1500 -75: [10:21:36] ------------------------------------- -75: [10:21:36] Test Reaction StructuralFingerprint -75: [10:21:36] ------------------------------------- -75: [10:21:36] Test Reaction DifferenceFingerprint - 73/208 Test #75: testReactionFingerprints ............... Passed 0.17 sec +75: [18:22:09] ------------------------------------- +75: [18:22:09] Test Reaction StructuralFingerprint +75: [18:22:09] ------------------------------------- +75: [18:22:09] Test Reaction DifferenceFingerprint + 72/208 Test #75: testReactionFingerprints ............... Passed 0.20 sec test 76 Start 76: testEnumeration @@ -31011,55 +31048,50 @@ 76: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions 76: Test timeout computed to be: 1500 76: 30000000 30000000 -58: [10:21:41] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [10:21:41] Warning: molecule is tagged as 3D, but all Z coords are zero -58: ---------------------------------- -58: ---------------------------------- -58: [10:21:41] -58: -58: **** -58: Pre-condition Violation -58: rlabel out of range for MDL files -58: Violation occurred on line 804 in file ./Code/GraphMol/Atom.cpp -58: Failed Expression: rlabel >= 0 && rlabel < 100 -58: **** -58: -58: [10:21:41] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -58: [10:21:42] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -58: [10:21:42] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -58: [10:21:42] Empty atom list: 'M ALS 1 0 F' on line 8. - 74/208 Test #58: fileParsersTest1 ....................... Passed 34.12 sec +61: [18:22:13] Finished: testSmiCorrectness() +61: [18:22:13] ----------------------------------------- +61: +61: [18:22:13] +61: ----------------------------------------- +61: [18:22:13] Spurious data before the first property will be ignored +61: [18:22:13] Property will be truncated after the first blank line +61: [18:22:13] Property will be truncated after the first blank line +61: [18:22:13] Property will be truncated after the first blank line +61: [18:22:15] Finished: testSDCorrectness() +61: [18:22:15] ----------------------------------------- +61: + 73/208 Test #61: testMultithreadedMolSupplier ........... Passed 40.17 sec test 77 Start 77: rxnTestCatch 77: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/rxnTestCatch 77: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions 77: Test timeout computed to be: 1500 -77: [10:21:42] atom 0 in product 0 has multiple charge specifications. -77: [10:21:42] mapped atoms in the reactants were not mapped in the products. +77: [18:22:16] atom 0 in product 0 has multiple charge specifications. +77: [18:22:16] mapped atoms in the reactants were not mapped in the products. 77: unmapped numbers are: 2 -77: [10:21:42] mapped atoms in the reactants were not mapped in the products. +77: [18:22:16] mapped atoms in the reactants were not mapped in the products. 77: unmapped numbers are: 2 -77: [10:21:42] SMARTS Parse Error: unclosed ring for input: 'CC1' -77: [10:21:42] SMILES Parse Error: unclosed ring for input: 'CC1' -77: [10:21:42] mapped atoms in the reactants were not mapped in the products. +77: [18:22:16] SMARTS Parse Error: unclosed ring for input: 'CC1' +77: [18:22:16] SMILES Parse Error: unclosed ring for input: 'CC1' +77: [18:22:16] mapped atoms in the reactants were not mapped in the products. 77: unmapped numbers are: 2 -77: [10:21:42] product atom-mapping number 2 not found in reactants. -77: [10:21:42] mapped atoms in the reactants were not mapped in the products. +77: [18:22:16] product atom-mapping number 2 not found in reactants. +77: [18:22:16] mapped atoms in the reactants were not mapped in the products. 77: unmapped numbers are: 2 -77: [10:21:42] product atom-mapping number 2 not found in reactants. -77: [10:21:42] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +77: [18:22:16] product atom-mapping number 2 not found in reactants. +77: [18:22:16] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 77: =============================================================================== 77: All tests passed (450 assertions in 14 test cases) 77: - 75/208 Test #77: rxnTestCatch ........................... Passed 0.31 sec + 74/208 Test #77: rxnTestCatch ........................... Passed 0.88 sec test 78 Start 78: pyChemReactions 78: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 78: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap 78: Test timeout computed to be: 1500 -78: [10:21:44] +78: [18:22:20] 78: 78: **** 78: Pre-condition Violation @@ -31068,7 +31100,7 @@ 78: Failed Expression: d_implicitValence > -1 78: **** 78: -78: [10:21:44] +78: [18:22:20] 78: 78: **** 78: Pre-condition Violation @@ -31077,98 +31109,98 @@ 78: Failed Expression: d_implicitValence > -1 78: **** 78: -78: ...[10:21:44] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [10:21:44] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [10:21:44] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [10:21:44] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: .[10:21:44] product atom-mapping number 1 found multiple times. -78: [10:21:44] product atom-mapping number 1 found multiple times. -78: ................[10:21:44] mapped atoms in the reactants were not mapped in the products. +78: ...[18:22:20] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [18:22:20] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [18:22:20] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [18:22:20] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: .[18:22:20] product atom-mapping number 1 found multiple times. +78: [18:22:20] product atom-mapping number 1 found multiple times. +78: ................[18:22:21] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -78: [10:21:44] mapped atoms in the reactants were not mapped in the products. +78: [18:22:21] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -78: .[10:21:44] mapped atoms in the reactants were not mapped in the products. +78: .[18:22:21] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 78: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:515: DeprecationWarning: Please use assertTrue instead. 78: self.failUnless(rxn) -78: [10:21:44] reactant 2 has no mapped atoms. -78: [10:21:44] reactant 2 has no mapped atoms. -78: [10:21:44] product 1 has no mapped atoms. +78: [18:22:21] reactant 2 has no mapped atoms. +78: [18:22:21] reactant 2 has no mapped atoms. +78: [18:22:21] product 1 has no mapped atoms. 78: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:558: DeprecationWarning: Please use assertEqual instead. 78: self.assertEquals(res, res2) -78: ......[10:21:44] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -78: [10:21:44] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -78: [10:21:44] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -78: [10:21:44] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -78: .[10:21:44] reactant atom-mapping number 1 found multiple times. -78: [10:21:44] product atom-mapping number 2 not found in reactants. -78: [10:21:44] mapped atoms in the reactants were not mapped in the products. +78: ......[18:22:21] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +78: [18:22:21] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +78: [18:22:21] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +78: [18:22:21] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +78: .[18:22:21] reactant atom-mapping number 1 found multiple times. +78: [18:22:21] product atom-mapping number 2 not found in reactants. +78: [18:22:21] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 4 -78: [10:21:44] product atom-mapping number 5 not found in reactants. +78: [18:22:21] product atom-mapping number 5 not found in reactants. 78: ........./build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:739: DeprecationWarning: Please use assertFalse instead. 78: self.failIf(rxn is None) 78: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> 78: png = open(fname, 'rb').read() 78: ResourceWarning: Enable tracemalloc to get the object allocation traceback -78: ..[10:21:44] SMARTS Parse Error: syntax error while parsing: boromicacid -78: [10:21:44] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -78: [10:21:44] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -78: [10:21:44] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -78: [10:21:44] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -78: [10:21:44] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -78: [10:21:44] reaction has no reactants -78: [10:21:44] reaction has no products -78: [10:21:44] initialization failed -78: [10:21:44] reaction has no reactants -78: [10:21:44] reaction has no products -78: .[10:21:44] SMARTS Parse Error: syntax error while parsing: boromicacid -78: [10:21:44] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -78: [10:21:44] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -78: [10:21:44] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -78: [10:21:44] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -78: [10:21:44] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -78: [10:21:44] reaction has no reactants -78: [10:21:44] reaction has no products -78: [10:21:44] initialization failed -78: [10:21:44] reaction has no reactants -78: [10:21:44] reaction has no products +78: ..[18:22:22] SMARTS Parse Error: syntax error while parsing: boromicacid +78: [18:22:22] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +78: [18:22:22] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +78: [18:22:22] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +78: [18:22:22] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +78: [18:22:22] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +78: [18:22:22] reaction has no reactants +78: [18:22:22] reaction has no products +78: [18:22:22] initialization failed +78: [18:22:22] reaction has no reactants +78: [18:22:22] reaction has no products +78: .[18:22:22] SMARTS Parse Error: syntax error while parsing: boromicacid +78: [18:22:22] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +78: [18:22:22] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +78: [18:22:22] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +78: [18:22:22] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +78: [18:22:22] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +78: [18:22:22] reaction has no reactants +78: [18:22:22] reaction has no products +78: [18:22:22] initialization failed +78: [18:22:22] reaction has no reactants +78: [18:22:22] reaction has no products 78: . 78: ---------------------------------------------------------------------- -78: Ran 45 tests in 0.632s +78: Ran 45 tests in 1.508s 78: 78: OK 78: ******************************************** 78: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -78: - 76/208 Test #78: pyChemReactions ........................ Passed 1.94 sec +78: + 75/208 Test #78: pyChemReactions ........................ Passed 6.11 sec test 79 Start 79: pyChemReactionEnumerations 79: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 79: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap 79: Test timeout computed to be: 1500 -79: [10:21:45] == testCartesianProduct +79: [18:22:24] == testCartesianProduct 79: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:62: DeprecationWarning: Please use assertEqual instead. 79: self.assertEquals(cartProd.GetNumPermutations(), 10*5*6) -79: .[10:21:46] == testEnumerateLibrary +79: .[18:22:25] == testEnumerateLibrary 79: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:268: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> 79: enumerator3.InitFromString(open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) 79: ResourceWarning: Enable tracemalloc to get the object allocation traceback -79: ..[10:21:46] == testRGroupState -79: .[10:21:46] == testRandomEnumerateAllBBsLibrary +79: ..[18:22:25] == testRGroupState +79: .[18:22:25] == testRandomEnumerateAllBBsLibrary 79: ** [1, 1] 79: ** [0, 2] 79: ** [1, 0] -79: .[10:21:46] == testRandomEnumerateLibrary -79: .[10:21:46] == testRandomSample -79: .[10:21:46] == testRandomSampleAllBBs -79: .[10:21:46] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -79: [10:21:46] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -79: .[10:21:46] == testRemoveBadMatches -79: .[10:21:46] == testTimings +79: .[18:22:25] == testRandomEnumerateLibrary +79: .[18:22:25] == testRandomSample +79: .[18:22:26] == testRandomSampleAllBBs +79: .[18:22:26] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +79: [18:22:26] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +79: .[18:22:26] == testRemoveBadMatches +79: .[18:22:26] == testTimings 79: . 79: ---------------------------------------------------------------------- -79: Ran 11 tests in 15.760s +79: Ran 11 tests in 43.850s 79: 79: OK 79: True @@ -31181,71 +31213,71 @@ 79: 0 10 out of 10 79: 1 5 out of 5 79: 2 6 out of 6 -79: Skipped 10000000 in 0.26299190521240234 seconds -79: Skipped 10000000 in 13.089159727096558 seconds -79: Skipped 10000000 in 1.109867811203003 seconds - 77/208 Test #79: pyChemReactionEnumerations ............. Passed 16.79 sec +79: Skipped 10000000 in 0.9767680168151855 seconds +79: Skipped 10000000 in 35.2315833568573 seconds +79: Skipped 10000000 in 4.087777137756348 seconds + 76/208 Test #79: pyChemReactionEnumerations ............. Passed 46.55 sec test 80 Start 80: pyChemReactionSanitize 80: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 80: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap 80: Test timeout computed to be: 1500 -80: .[10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. +80: .[18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. 80: ./build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py:287: DeprecationWarning: Please use assertEqual instead. 80: self.assertEquals(res, good_res) -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] reactant 0 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] product 0 has no mapped atoms. -80: [10:22:02] Could not find RLabel mapping for atom: 0 in template: 1 -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. -80: [10:22:02] reactant 1 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] reactant 0 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] product 0 has no mapped atoms. +80: [18:23:12] Could not find RLabel mapping for atom: 0 in template: 1 +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. +80: [18:23:12] reactant 1 has no mapped atoms. 80: () 80: ******************************************** 80: $RXN @@ -31565,7 +31597,7 @@ 80: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 80: .. 80: ---------------------------------------------------------------------- -80: Ran 4 tests in 0.092s +80: Ran 4 tests in 0.168s 80: 80: OK 80: $RXN @@ -31612,7 +31644,7 @@ 80: M END 80: 80: $RXN Failed - 78/208 Test #80: pyChemReactionSanitize ................. Passed 1.09 sec + 77/208 Test #80: pyChemReactionSanitize ................. Passed 3.39 sec test 81 Start 81: testChemTransforms @@ -31627,17 +31659,17 @@ 81: replaceSub smi1:CCNCC 81: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 81: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -81: [10:22:03] SMARTS Parse Error: syntax error while parsing: bar -81: [10:22:03] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' - 79/208 Test #81: testChemTransforms ..................... Passed 0.28 sec +81: [18:23:13] SMARTS Parse Error: syntax error while parsing: bar +81: [18:23:13] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' + 78/208 Test #81: testChemTransforms ..................... Passed 0.79 sec test 82 Start 82: chemTransformsTestCatch 82: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 82: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms 82: Test timeout computed to be: 1500 -82: [10:22:03] Incomplete atom labelling, cannot make bond -82: [10:22:03] +82: [18:23:13] Incomplete atom labelling, cannot make bond +82: [18:23:13] 82: 82: **** 82: Invariant Violation @@ -31646,8 +31678,8 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [10:22:03] Incomplete atom labelling, cannot make bond -82: [10:22:03] +82: [18:23:14] Incomplete atom labelling, cannot make bond +82: [18:23:14] 82: 82: **** 82: Invariant Violation @@ -31656,8 +31688,8 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [10:22:03] Incomplete atom labelling, cannot make bond -82: [10:22:03] +82: [18:23:14] Incomplete atom labelling, cannot make bond +82: [18:23:14] 82: 82: **** 82: Invariant Violation @@ -31666,10 +31698,10 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [10:22:03] Incomplete atom labelling, cannot make bond -82: [10:22:03] Incomplete atom labelling, cannot make bond -82: [10:22:03] Incomplete atom labelling, cannot make bond -82: [10:22:03] +82: [18:23:14] Incomplete atom labelling, cannot make bond +82: [18:23:14] Incomplete atom labelling, cannot make bond +82: [18:23:14] Incomplete atom labelling, cannot make bond +82: [18:23:14] 82: 82: **** 82: Invariant Violation @@ -31678,8 +31710,8 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [10:22:03] Incomplete atom labelling, cannot make bond -82: [10:22:03] +82: [18:23:14] Incomplete atom labelling, cannot make bond +82: [18:23:14] 82: 82: **** 82: Invariant Violation @@ -31688,7 +31720,7 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [10:22:03] +82: [18:23:14] 82: 82: **** 82: Invariant Violation @@ -31700,7 +31732,7 @@ 82: =============================================================================== 82: All tests passed (531 assertions in 4 test cases) 82: - 80/208 Test #82: chemTransformsTestCatch ................ Passed 0.46 sec + 79/208 Test #82: chemTransformsTestCatch ................ Passed 1.06 sec test 83 Start 83: tautomerQueryTestCatch @@ -31710,7 +31742,7 @@ 83: =============================================================================== 83: All tests passed (86 assertions in 12 test cases) 83: - 81/208 Test #83: tautomerQueryTestCatch ................. Passed 0.84 sec + 80/208 Test #83: tautomerQueryTestCatch ................. Passed 2.37 sec test 84 Start 84: pyTautomerQuery @@ -31719,10 +31751,10 @@ 84: Test timeout computed to be: 1500 84: ..... 84: ---------------------------------------------------------------------- -84: Ran 5 tests in 0.137s +84: Ran 5 tests in 0.550s 84: 84: OK - 82/208 Test #84: pyTautomerQuery ........................ Passed 1.08 sec + 81/208 Test #84: pyTautomerQuery ........................ Passed 4.11 sec test 85 Start 85: testSubgraphs1 @@ -31756,7 +31788,7 @@ 85: ----------------------- 85: testRootedPaths 85: Finished - 83/208 Test #85: testSubgraphs1 ......................... Passed 1.09 sec + 82/208 Test #85: testSubgraphs1 ......................... Passed 3.88 sec test 86 Start 86: testSubgraphs2 @@ -31778,7 +31810,7 @@ 86: ----------------------- 86: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 86: Finished - 84/208 Test #86: testSubgraphs2 ......................... Passed 0.13 sec + 83/208 Test #86: testSubgraphs2 ......................... Passed 0.21 sec test 87 Start 87: filterCatalogTest @@ -31879,7 +31911,7 @@ 87: 0 hzone_phenol_A(479) 87: 1 cyano_imine_B(17) 87: 2 keto_keto_gamma(5) - 85/208 Test #87: filterCatalogTest ...................... Passed 0.78 sec + 84/208 Test #87: filterCatalogTest ...................... Passed 2.15 sec test 88 Start 88: pyFilterCatalog @@ -31888,101 +31920,101 @@ 88: Test timeout computed to be: 1500 88: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py:172: DeprecationWarning: Please use assertEqual instead. 88: self.assertEquals(entry.GetProp(key), "PAINS_A") -88: ...........[10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: [10:22:11] SMILES Parse Error: syntax error while parsing: --- -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [10:22:11] dasfsadf -88: .[10:22:11] SMILES Parse Error: syntax error while parsing: mydoghasfleas -88: [10:22:11] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +88: ...........[18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: [18:23:41] SMILES Parse Error: syntax error while parsing: --- +88: [18:23:41] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [18:23:41] dasfsadf +88: .[18:23:42] SMILES Parse Error: syntax error while parsing: mydoghasfleas +88: [18:23:42] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' 88: ...... 88: ---------------------------------------------------------------------- -88: Ran 20 tests in 2.987s +88: Ran 20 tests in 12.011s 88: 88: OK 88: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -32004,7 +32036,7 @@ 88: 1 88: 2 88: running - 86/208 Test #88: pyFilterCatalog ........................ Passed 4.05 sec + 85/208 Test #88: pyFilterCatalog ........................ Passed 16.89 sec test 89 Start 89: testFragCatalog @@ -32012,7 +32044,7 @@ 89: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog 89: Test timeout computed to be: 1500 89: 21 -89: [10:22:14] +89: [18:23:54] 89: 89: **** 89: Invariant Violation @@ -32021,7 +32053,7 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: -89: [10:22:14] +89: [18:23:54] 89: 89: **** 89: Invariant Violation @@ -32030,7 +32062,7 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: -89: [10:22:14] +89: [18:23:54] 89: 89: **** 89: Invariant Violation @@ -32039,7 +32071,7 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: - 87/208 Test #89: testFragCatalog ........................ Passed 3.05 sec + 86/208 Test #89: testFragCatalog ........................ Passed 9.88 sec test 90 Start 90: pyFragCatalog @@ -32048,54 +32080,54 @@ 90: Test timeout computed to be: 1500 90: ......... 90: ---------------------------------------------------------------------- -90: Ran 9 tests in 0.258s +90: Ran 9 tests in 0.676s 90: 90: OK - 88/208 Test #90: pyFragCatalog .......................... Passed 1.23 sec + 87/208 Test #90: pyFragCatalog .......................... Passed 4.86 sec test 91 Start 91: testDescriptors 91: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testDescriptors 91: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 91: Test timeout computed to be: 1500 -91: [10:22:15] ------------------------------------- -91: [10:22:15] Test Crippen parameter acquisition. -91: [10:22:15] done -91: [10:22:15] ------------------------------------- -91: [10:22:15] Test Crippen calculation. -91: [10:22:15] done -91: [10:22:15] ------------------------------------- -91: [10:22:15] Test Issue262: problems with Crippen calculation from pickles. -91: [10:22:15] done -91: [10:22:15] ------------------------------------- -91: [10:22:15] Test AMW calculation. -91: [10:22:15] done -91: [10:22:15] ------------------------------------- -91: [10:22:15] Test Exact MW calculation. -91: [10:22:15] done -91: [10:22:15] ------------------------------------- -91: [10:22:15] Test Labute ASA descriptors. -91: [10:22:15] done -91: [10:22:15] ------------------------------------- -91: [10:22:15] Test TPSA descriptors. -91: [10:22:16] done -91: [10:22:16] ------------------------------------- -91: [10:22:16] Test Lipinski parameters. -91: [10:22:16] done -91: [10:22:16] ------------------------------------- -91: [10:22:16] Test VSA descriptors. -91: [10:22:16] done -91: [10:22:16] ------------------------------------- -91: [10:22:16] Test molecular formula calculation. -91: [10:22:16] done -91: [10:22:16] ------------------------------------- -91: [10:22:16] Test Issue 3415534. -91: [10:22:16] done -91: [10:22:16] ------------------------------------- -91: [10:22:16] Test Issue3433771: Bad definition for Crippen atom type O11. -91: [10:22:16] done -91: [10:22:16] ------------------------------------- -91: [10:22:16] Test multithreading +91: [18:23:59] ------------------------------------- +91: [18:23:59] Test Crippen parameter acquisition. +91: [18:23:59] done +91: [18:23:59] ------------------------------------- +91: [18:23:59] Test Crippen calculation. +91: [18:23:59] done +91: [18:23:59] ------------------------------------- +91: [18:23:59] Test Issue262: problems with Crippen calculation from pickles. +91: [18:23:59] done +91: [18:23:59] ------------------------------------- +91: [18:23:59] Test AMW calculation. +91: [18:23:59] done +91: [18:23:59] ------------------------------------- +91: [18:23:59] Test Exact MW calculation. +91: [18:23:59] done +91: [18:23:59] ------------------------------------- +91: [18:23:59] Test Labute ASA descriptors. +91: [18:23:59] done +91: [18:23:59] ------------------------------------- +91: [18:23:59] Test TPSA descriptors. +91: [18:23:59] done +91: [18:23:59] ------------------------------------- +91: [18:23:59] Test Lipinski parameters. +91: [18:24:01] done +91: [18:24:01] ------------------------------------- +91: [18:24:01] Test VSA descriptors. +91: [18:24:01] done +91: [18:24:01] ------------------------------------- +91: [18:24:01] Test molecular formula calculation. +91: [18:24:01] done +91: [18:24:01] ------------------------------------- +91: [18:24:01] Test Issue 3415534. +91: [18:24:01] done +91: [18:24:01] ------------------------------------- +91: [18:24:01] Test Issue3433771: Bad definition for Crippen atom type O11. +91: [18:24:01] done +91: [18:24:01] ------------------------------------- +91: [18:24:01] Test multithreading 91: reading molecules 91: processing 91: launch :0 @@ -32108,144 +32140,144 @@ 76: 1,1 0 76: 2,0 0 76: 2,1 0 - 89/208 Test #76: testEnumeration ........................ Passed 50.25 sec + 88/208 Test #76: testEnumeration ........................ Passed 139.34 sec test 92 Start 92: testAUTOCORR2D 92: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testAUTOCORR2D 92: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 92: Test timeout computed to be: 1500 -92: [10:22:27] ---------------------------- +92: [18:24:28] ---------------------------- 92: start test autocorr2D -92: [10:22:28] done -92: [10:22:28] ------------------------------------- -92: [10:22:28] Test Github #3806: NaNs from AUTOCORR2D descriptor -92: [10:22:28] done - 90/208 Test #92: testAUTOCORR2D ......................... Passed 1.59 sec +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test Issue252: Bad definitions for Crippen atom types. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test calculation of ChiVs. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test calculation of ChiNs. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test calculation of HallKierAlpha. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test calculation of Kappa1. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test calculation of Kappa2. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test calculation of Kappa3. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test Crippen atom type calculations. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test ring descriptors +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test other count descriptors. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test MQN +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test GitHub Issue 56. +91: [18:24:32] WARNING: not removing hydrogen atom without neighbors +91: [18:24:32] WARNING: not removing hydrogen atom without neighbors +91: [18:24:32] WARNING: not removing hydrogen atom without neighbors +91: [18:24:32] WARNING: not removing hydrogen atom without neighbors +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test Github92: Bad Crippen atom type for pyrrole H. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test Github362: order dependence in Kier-Hall descriptors. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test calculation of spiro and bridgehead counts. +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test Github694: ExactMolWt ignoring the mass of the electron +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Testing Properties and KitchenSink +91: [18:24:32] ---Caught keyerror (bad property name)--- +91: [18:24:32] ---Caught stereo value error--- +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test USR Descriptor +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test Github #1973: support P and S terms for TPSA calculation +91: [18:24:32] done +91: [18:24:32] ------------------------------------- +91: [18:24:32] Test Github #2948: Empty molecule has non-zero LabuteASA +91: [18:24:32] done + 89/208 Test #91: testDescriptors ........................ Passed 33.73 sec test 93 Start 93: testATF 93: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testATF 93: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 93: Test timeout computed to be: 1500 - 91/208 Test #93: testATF ................................ Passed 0.12 sec +92: [18:24:32] done +92: [18:24:32] ------------------------------------- +92: [18:24:32] Test Github #3806: NaNs from AUTOCORR2D descriptor +92: [18:24:32] done + 90/208 Test #93: testATF ................................ Passed 0.22 sec test 94 Start 94: testBCUT 94: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testBCUT 94: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 94: Test timeout computed to be: 1500 -94: [10:22:28] ------------------------------------- -94: [10:22:28] Basic BCUT tests. -94: [10:22:28] done -94: [10:22:28] ------------------------------------- -94: [10:22:28] Larger BCUT tests. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test Issue252: Bad definitions for Crippen atom types. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test calculation of ChiVs. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test calculation of ChiNs. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test calculation of HallKierAlpha. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test calculation of Kappa1. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test calculation of Kappa2. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test calculation of Kappa3. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test Crippen atom type calculations. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test ring descriptors -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test other count descriptors. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test MQN -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test GitHub Issue 56. -91: [10:22:31] WARNING: not removing hydrogen atom without neighbors -91: [10:22:31] WARNING: not removing hydrogen atom without neighbors -91: [10:22:31] WARNING: not removing hydrogen atom without neighbors -91: [10:22:31] WARNING: not removing hydrogen atom without neighbors -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test Github92: Bad Crippen atom type for pyrrole H. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test Github362: order dependence in Kier-Hall descriptors. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test calculation of spiro and bridgehead counts. -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test Github694: ExactMolWt ignoring the mass of the electron -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Testing Properties and KitchenSink -91: [10:22:31] ---Caught keyerror (bad property name)--- -91: [10:22:31] ---Caught stereo value error--- -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test USR Descriptor -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test Github #1973: support P and S terms for TPSA calculation -91: [10:22:31] done -91: [10:22:31] ------------------------------------- -91: [10:22:31] Test Github #2948: Empty molecule has non-zero LabuteASA -91: [10:22:31] done - 92/208 Test #91: testDescriptors ........................ Passed 15.35 sec + 91/208 Test #92: testAUTOCORR2D ......................... Passed 4.44 sec test 95 Start 95: testEEM 95: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testEEM 95: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 95: Test timeout computed to be: 1500 - 93/208 Test #94: testBCUT ............................... Passed 2.49 sec +94: [18:24:33] ------------------------------------- +94: [18:24:33] Basic BCUT tests. +94: [18:24:33] done +94: [18:24:33] ------------------------------------- +94: [18:24:33] Larger BCUT tests. + 92/208 Test #94: testBCUT ............................... Passed 5.18 sec test 96 Start 96: testPBF 96: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testPBF 96: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 96: Test timeout computed to be: 1500 -96: [10:22:31] ------------------------------------- -96: [10:22:31] Basic PBF tests. -96: [10:22:32] done -96: [10:22:32] ------------------------------------- -96: [10:22:32] PBF edge cases. -96: [10:22:32] done - 94/208 Test #96: testPBF ................................ Passed 0.81 sec -test 97 - Start 97: testRDFcustom - -97: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testRDFcustom -97: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors -97: Test timeout computed to be: 1500 +96: [18:24:38] ------------------------------------- +96: [18:24:38] Basic PBF tests. 95: =>start test EEM 95: 0 95: 100 95: 200 95: 300 95: 400 -95: Elapsed time: 2.27906 s +95: Elapsed time: 6.9887 s 95: Errors:0 -95: [10:22:33] test on : 500 molecules done - 95/208 Test #95: testEEM ................................ Passed 2.33 sec +95: [18:24:40] test on : 500 molecules done + 93/208 Test #95: testEEM ................................ Passed 7.16 sec +test 97 + Start 97: testRDFcustom + +97: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testRDFcustom +97: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors +97: Test timeout computed to be: 1500 +96: [18:24:40] done +96: [18:24:40] ------------------------------------- +96: [18:24:40] PBF edge cases. +96: [18:24:40] done + 94/208 Test #96: testPBF ................................ Passed 2.45 sec test 98 Start 98: testRDF @@ -32253,10 +32285,10 @@ 98: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 98: Test timeout computed to be: 1500 97: =>start test rdf custom -97: [10:22:33] test on : 365 molecules done +97: [18:24:44] test on : 365 molecules done 98: =>start test rdf -98: [10:22:35] test on : 365 molecules done - 96/208 Test #98: testRDF ................................ Passed 1.97 sec +98: [18:24:46] test on : 365 molecules done + 95/208 Test #98: testRDF ................................ Passed 5.56 sec test 99 Start 99: testMORSE @@ -32264,57 +32296,57 @@ 99: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 99: Test timeout computed to be: 1500 97: =>start test morse custom -97: [10:22:36] test on : 365 molecules done -97: =>start test AUTOCORR3D custom -97: [10:22:38] test on : 365 molecules done +97: [18:24:50] test on : 365 molecules done 99: =>start test MORSE 99: =>read file -99: [10:22:38] test on : 365 molecules done - 97/208 Test #99: testMORSE .............................. Passed 2.64 sec +99: [18:24:54] test on : 365 molecules done + 96/208 Test #99: testMORSE .............................. Passed 7.96 sec test 100 Start 100: test3D 100: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/test3D 100: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 100: Test timeout computed to be: 1500 -100: [10:22:38] ------------------------------------- -100: [10:22:38] Basic PMI tests. +100: [18:24:54] ------------------------------------- +100: [18:24:54] Basic PMI tests. +97: =>start test AUTOCORR3D custom +97: [18:24:55] test on : 365 molecules done +100: [18:24:56] done +100: [18:24:56] ------------------------------------- +100: [18:24:56] More PMI/NPR tests. +100: [18:24:56] done +100: [18:24:56] ------------------------------------- +100: [18:24:56] Basic NPR tests. 97: =>start test 2 WHIM custom -97: [10:22:39] test on : 365 molecules done -100: [10:22:39] done -100: [10:22:39] ------------------------------------- -100: [10:22:39] More PMI/NPR tests. -100: [10:22:39] done -100: [10:22:39] ------------------------------------- -100: [10:22:39] Basic NPR tests. -97: =>start test 1 WHIM custom -97: [10:22:39] test on : 365 molecules done -100: [10:22:40] done -100: [10:22:40] ------------------------------------- -100: [10:22:40] PMI edge cases. -100: [10:22:40] done -100: [10:22:40] ------------------------------------- -100: [10:22:40] NPR edge cases. -100: [10:22:40] done -100: [10:22:40] ------------------------------------- -100: [10:22:40] 3D descriptors. -100: [10:22:40] done -100: [10:22:40] ------------------------------------- -100: [10:22:40] 3D descriptor edge cases. -100: [10:22:40] done -100: [10:22:40] ------------------------------------- -100: [10:22:40] Inertial shape factor. -100: [10:22:40] done - 98/208 Test #100: test3D ................................. Passed 2.01 sec +97: [18:24:58] test on : 365 molecules done +100: [18:24:59] done +100: [18:24:59] ------------------------------------- +100: [18:24:59] PMI edge cases. +100: [18:24:59] done +100: [18:24:59] ------------------------------------- +100: [18:24:59] NPR edge cases. +100: [18:24:59] done +100: [18:24:59] ------------------------------------- +100: [18:24:59] 3D descriptors. +100: [18:24:59] done +100: [18:24:59] ------------------------------------- +100: [18:24:59] 3D descriptor edge cases. +100: [18:24:59] done +100: [18:24:59] ------------------------------------- +100: [18:24:59] Inertial shape factor. +100: [18:24:59] done + 97/208 Test #100: test3D ................................. Passed 5.25 sec test 101 Start 101: testWHIM 101: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testWHIM 101: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 +97: =>start test 1 WHIM custom +97: [18:25:00] test on : 365 molecules done 101: =>start test WHIM -101: [10:22:41] test on : 365 molecules done - 99/208 Test #101: testWHIM ............................... Passed 1.43 sec +101: [18:25:03] test on : 365 molecules done + 98/208 Test #101: testWHIM ............................... Passed 3.90 sec test 102 Start 102: testGETAWAY @@ -32322,17 +32354,17 @@ 102: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 97: =>start test GETAWAY custom -97: [10:22:45] test on : 365 molecules done -100/208 Test #97: testRDFcustom .......................... Passed 13.80 sec +97: [18:25:17] test on : 365 molecules done + 99/208 Test #97: testRDFcustom .......................... Passed 37.45 sec test 103 Start 103: testAUTOCORR3D 103: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testAUTOCORR3D 103: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 -103: =>start test autocorr3D -103: [10:22:47] test on : 365 molecules done -101/208 Test #103: testAUTOCORR3D ......................... Passed 1.40 sec +102: =>start test GETAWAY +102: [18:25:18] test on : 365 molecules done +100/208 Test #102: testGETAWAY ............................ Passed 15.66 sec test 104 Start 104: testCoulombMat @@ -32341,7 +32373,7 @@ 104: Test timeout computed to be: 1500 104: ===================== Testing CoulombMat ======================= 104: CM test 1 mat Done -102/208 Test #104: testCoulombMat ......................... Passed 0.12 sec +101/208 Test #104: testCoulombMat ......................... Passed 0.20 sec test 105 Start 105: descriptorsTestCatch @@ -32351,23 +32383,14 @@ 105: =============================================================================== 105: All tests passed (130 assertions in 5 test cases) 105: -103/208 Test #105: descriptorsTestCatch ................... Passed 0.14 sec +102/208 Test #105: descriptorsTestCatch ................... Passed 0.32 sec test 106 Start 106: pyMolDescriptors 106: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 106: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap 106: Test timeout computed to be: 1500 -102: =>start test GETAWAY -102: [10:22:47] test on : 365 molecules done -104/208 Test #102: testGETAWAY ............................ Passed 6.27 sec -test 107 - Start 107: pyMolDescriptors3D - -107: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/test3D.py" -107: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap -107: Test timeout computed to be: 1500 -106: .....[10:22:48] +106: .....[18:25:21] 106: 106: **** 106: Pre-condition Violation @@ -32378,7 +32401,7 @@ 106: 106: ........................ 106: ---------------------------------------------------------------------- -106: Ran 29 tests in 0.132s +106: Ran 29 tests in 0.282s 106: 106: OK 106: exactmw 78.046950192 @@ -32426,7 +32449,16 @@ 106: Phi 0.9130327103921437 106: exactmw 78.046950192 106: lipinskiHBA 0.0 -105/208 Test #106: pyMolDescriptors ....................... Passed 1.34 sec +103/208 Test #106: pyMolDescriptors ....................... Passed 2.63 sec +test 107 + Start 107: pyMolDescriptors3D + +107: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/test3D.py" +107: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap +107: Test timeout computed to be: 1500 +103: =>start test autocorr3D +103: [18:25:22] test on : 365 molecules done +104/208 Test #103: testAUTOCORR3D ......................... Passed 4.94 sec test 108 Start 108: testFingerprints @@ -32916,222 +32948,222 @@ 108: 108: ------------------- 108: -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Morgan Fingerprints. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Morgan Fingerprints using fromAtoms argument. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Morgan Fingerprints as bit vects. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Morgan Fingerprints with feature invariants. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test additional Morgan fingerprints options. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Atom Codes. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Atom Pairs. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Atom Pairs part 2. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Topological Torsions. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Bulk Topological Torsions. +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Morgan Fingerprints. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Morgan Fingerprints using fromAtoms argument. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Morgan Fingerprints as bit vects. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Morgan Fingerprints with feature invariants. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test additional Morgan fingerprints options. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Atom Codes. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Atom Pairs. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Atom Pairs part 2. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Topological Torsions. +108: [18:25:22] done +108: [18:25:22] ------------------------------------- +108: [18:25:22] Test Bulk Topological Torsions. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test Hashed Atom Pairs. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test Hashed torsions. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test Rooted Atom Pairs. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test ignoring atoms in Atom Pairs. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test Rooted Topological Torsions. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test ignoring atoms in Topological Torsions. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test atom info from morgan fingerprints. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test atom info from morgan fingerprints including Info Redundant Environments. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] ------------------------------------- +108: [18:25:23] ------------------------------------- +108: [18:25:23] ------------------------------------- +108: [18:25:23] ------------------------------------- +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test Atom Pairs including info about chirality. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test Topological Torsions including info about chirality. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test GitHub Issue 25: fingerprint backwards compatibility. +108: [18:25:23] done +108: [18:25:23] ------------------------------------- +108: [18:25:23] Test GitHub Issue 151: PatternFingerprint problems +108: [18:25:24] done +108: [18:25:24] ------------------------------------- +108: [18:25:24] Test 3D atom pairs. +108: [18:25:24] done +108: [18:25:24] ------------------------------------- +108: [18:25:24] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +108: [18:25:24] done +108: [18:25:24] ------------------------------------- +108: [18:25:24] Test multithreading with the pattern FP +108: reading molecules +108: pass 1 +108: launch :0 +108: launch :1 +108: launch :2 +108: launch :3 +108: pass 2 +108: launch :0 +108: launch :1 +108: launch :2 +108: launch :3 107: ........ 107: ---------------------------------------------------------------------- -107: Ran 8 tests in 0.639s +107: Ran 8 tests in 2.474s 107: 107: OK -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Hashed Atom Pairs. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Hashed torsions. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Rooted Atom Pairs. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test ignoring atoms in Atom Pairs. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Rooted Topological Torsions. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test ignoring atoms in Topological Torsions. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test atom info from morgan fingerprints. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test atom info from morgan fingerprints including Info Redundant Environments. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] ------------------------------------- -108: [10:22:49] ------------------------------------- -108: [10:22:49] ------------------------------------- -108: [10:22:49] ------------------------------------- -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Atom Pairs including info about chirality. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test Topological Torsions including info about chirality. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test GitHub Issue 25: fingerprint backwards compatibility. -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test GitHub Issue 151: PatternFingerprint problems -106/208 Test #107: pyMolDescriptors3D ..................... Passed 1.66 sec +105/208 Test #107: pyMolDescriptors3D ..................... Passed 5.83 sec test 109 Start 109: testMHFPFingerprint 109: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/testMHFPFingerprint 109: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints 109: Test timeout computed to be: 1500 -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test 3D atom pairs. -109: [10:22:49] ------------------------------------- -109: [10:22:49] Test MHFP fingerprint encoder initialization -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -108: [10:22:49] done -108: [10:22:49] ------------------------------------- -108: [10:22:49] Test multithreading with the pattern FP -108: reading molecules -109: [10:22:49] done -109: [10:22:49] ------------------------------------- -109: [10:22:49] Test MHFP shingling creation -108: pass 1 -108: launch :0 -108: launch :1 -108: launch :2 -108: launch :3 -109: [10:22:49] done -109: [10:22:49] ------------------------------------- -109: [10:22:49] Test MHFP hashing of string and uint arrays -109: [10:22:49] done -109: [10:22:49] ------------------------------------- -109: [10:22:49] Test SECFP fingerprint functionality -109: [10:22:49] done -107/208 Test #109: testMHFPFingerprint .................... Passed 0.25 sec +109: [18:25:28] ------------------------------------- +109: [18:25:28] Test MHFP fingerprint encoder initialization +109: [18:25:28] done +109: [18:25:28] ------------------------------------- +109: [18:25:28] Test MHFP shingling creation +109: [18:25:28] done +109: [18:25:28] ------------------------------------- +109: [18:25:28] Test MHFP hashing of string and uint arrays +109: [18:25:28] done +109: [18:25:28] ------------------------------------- +109: [18:25:28] Test SECFP fingerprint functionality +109: [18:25:28] done +106/208 Test #109: testMHFPFingerprint .................... Passed 0.43 sec test 110 Start 110: testFingerprintGenerators 110: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/testFingerprintGenerators 110: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints 110: Test timeout computed to be: 1500 -110: [10:22:49] ------------------------------------- -110: [10:22:49] Test atom-pair fp generator -110: [10:22:49] done -110: [10:22:49] ------------------------------------- -110: [10:22:49] Test atom-pair fp generator with different arguments -110: [10:22:49] done -110: [10:22:49] ------------------------------------- -110: [10:22:49] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test atom-pair additional output -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test Folded Atom Pairs. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test Rooted Atom Pairs. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test ignoring atoms in Atom Pairs. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test Atom Pairs including info about chirality. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test Morgan Fingerprints. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test morgan fp generator -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test Morgan Fingerprints using fromAtoms argument. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test Morgan Fingerprints as bit vects. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test Morgan Fingerprints with feature invariants. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test additional Morgan fingerprints options. -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Single atoms setting radius 1 bits in Morgan fingerprints -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test different invariant generator combinations -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test invariant overriding -110: [10:22:50] done -110: [10:22:50] ------------------------------------- -110: [10:22:50] Test RDKit fp generator -108: pass 2 -108: launch :0 -108: launch :1 -108: launch :2 -108: launch :3 -110: [10:22:51] done -110: [10:22:51] ------------------------------------- -110: [10:22:51] Test unfolded version of RDKFP -110: [10:22:51] ------------------------------------- -110: [10:22:51] Test topological torsion fp generator -110: [10:22:51] done -110: [10:22:51] ------------------------------------- -110: [10:22:51] Test Topological Torsions. -110: [10:22:51] done -110: [10:22:51] ------------------------------------- -110: [10:22:51] Test Folded torsions. -110: [10:22:51] done -110: [10:22:51] ------------------------------------- -110: [10:22:51] Test Bulk Topological Torsions. -110: [10:22:52] done -110: [10:22:52] ------------------------------------- -110: [10:22:52] Test Rooted Topological Torsions. -110: [10:22:52] done -110: [10:22:52] ------------------------------------- -110: [10:22:52] Test ignoring atoms in Topological Torsions. -110: [10:22:52] done -110: [10:22:52] ------------------------------------- -110: [10:22:52] ------------------------------------- -110: [10:22:52] Test Topological Torsions including info about chirality. -110: [10:22:52] done -110: [10:22:52] ------------------------------------- -110: [10:22:52] Test GitHub Issue 25: fingerprint backwards compatibility. -110: [10:22:52] done -110: [10:22:52] ------------------------------------- -110: [10:22:52] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -110: [10:22:52] done -110: [10:22:52] ------------------------------------- -110: [10:22:52] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -110: [10:22:52] Warning: molecule is tagged as 3D, but all Z coords are zero -110: [10:22:52] done -110: [10:22:52] ------------------------------------- -110: [10:22:52] Test convenience and bulk fp calculation functions -110: [10:22:54] done -108/208 Test #110: testFingerprintGenerators .............. Passed 4.82 sec +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test atom-pair fp generator +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test atom-pair fp generator with different arguments +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test atom-pair additional output +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test Folded Atom Pairs. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test Rooted Atom Pairs. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test ignoring atoms in Atom Pairs. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test Atom Pairs including info about chirality. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test Morgan Fingerprints. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test morgan fp generator +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test Morgan Fingerprints using fromAtoms argument. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test Morgan Fingerprints as bit vects. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test Morgan Fingerprints with feature invariants. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test additional Morgan fingerprints options. +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Single atoms setting radius 1 bits in Morgan fingerprints +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test different invariant generator combinations +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test invariant overriding +110: [18:25:28] done +110: [18:25:28] ------------------------------------- +110: [18:25:28] Test RDKit fp generator +110: [18:25:31] done +110: [18:25:31] ------------------------------------- +110: [18:25:31] Test unfolded version of RDKFP +110: [18:25:31] ------------------------------------- +110: [18:25:31] Test topological torsion fp generator +110: [18:25:31] done +110: [18:25:31] ------------------------------------- +110: [18:25:31] Test Topological Torsions. +110: [18:25:31] done +110: [18:25:31] ------------------------------------- +110: [18:25:31] Test Folded torsions. +110: [18:25:31] done +110: [18:25:31] ------------------------------------- +110: [18:25:31] Test Bulk Topological Torsions. +110: [18:25:32] done +110: [18:25:32] ------------------------------------- +110: [18:25:32] Test Rooted Topological Torsions. +110: [18:25:32] done +110: [18:25:32] ------------------------------------- +110: [18:25:32] Test ignoring atoms in Topological Torsions. +110: [18:25:32] done +110: [18:25:32] ------------------------------------- +110: [18:25:32] ------------------------------------- +110: [18:25:32] Test Topological Torsions including info about chirality. +110: [18:25:32] done +110: [18:25:32] ------------------------------------- +110: [18:25:32] Test GitHub Issue 25: fingerprint backwards compatibility. +110: [18:25:32] done +110: [18:25:32] ------------------------------------- +110: [18:25:32] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +110: [18:25:32] done +110: [18:25:32] ------------------------------------- +110: [18:25:32] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +110: [18:25:32] Warning: molecule is tagged as 3D, but all Z coords are zero +110: [18:25:32] done +110: [18:25:32] ------------------------------------- +110: [18:25:32] Test convenience and bulk fp calculation functions +110: [18:25:36] done +107/208 Test #110: testFingerprintGenerators .............. Passed 8.00 sec test 111 Start 111: fpTestCatch @@ -33141,7 +33173,7 @@ 111: =============================================================================== 111: All tests passed (163 assertions in 13 test cases) 111: -109/208 Test #111: fpTestCatch ............................ Passed 0.20 sec +108/208 Test #111: fpTestCatch ............................ Passed 0.38 sec test 112 Start 112: pyTestGenerator @@ -33150,10 +33182,10 @@ 112: Test timeout computed to be: 1500 112: ......... 112: ---------------------------------------------------------------------- -112: Ran 9 tests in 0.320s +112: Ran 9 tests in 0.536s 112: 112: OK -110/208 Test #112: pyTestGenerator ........................ Passed 2.07 sec +109/208 Test #112: pyTestGenerator ........................ Passed 3.57 sec test 113 Start 113: pyTestMHFP @@ -33162,17 +33194,17 @@ 113: Test timeout computed to be: 1500 113: . 113: ---------------------------------------------------------------------- -113: Ran 1 test in 0.176s +113: Ran 1 test in 0.446s 113: 113: OK -111/208 Test #113: pyTestMHFP ............................. Passed 1.79 sec +110/208 Test #113: pyTestMHFP ............................. Passed 3.64 sec test 114 Start 114: testPartialCharges 114: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/testPartialCharges 114: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges 114: Test timeout computed to be: 1500 -112/208 Test #114: testPartialCharges ..................... Passed 0.12 sec +111/208 Test #114: testPartialCharges ..................... Passed 0.20 sec test 115 Start 115: pyPartialCharges @@ -33181,10 +33213,10 @@ 115: Test timeout computed to be: 1500 115: ....... 115: ---------------------------------------------------------------------- -115: Ran 7 tests in 0.758s +115: Ran 7 tests in 1.403s 115: 115: OK -113/208 Test #115: pyPartialCharges ....................... Passed 2.18 sec +112/208 Test #115: pyPartialCharges ....................... Passed 4.18 sec test 116 Start 116: testMolTransforms @@ -33221,7 +33253,7 @@ 116: testWeightedCentroid 116: 116: *********************************************************** -114/208 Test #116: testMolTransforms ...................... Passed 0.13 sec +113/208 Test #116: testMolTransforms ...................... Passed 0.43 sec test 117 Start 117: pyMolTransforms @@ -33230,238 +33262,142 @@ 117: Test timeout computed to be: 1500 117: ........ 117: ---------------------------------------------------------------------- -117: Ran 8 tests in 0.210s +117: Ran 8 tests in 0.398s 117: 117: OK -115/208 Test #117: pyMolTransforms ........................ Passed 1.37 sec +114/208 Test #117: pyMolTransforms ........................ Passed 3.82 sec test 118 Start 118: testMMFFForceFieldHelpers 118: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 118: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF 118: Test timeout computed to be: 1500 -118: [10:23:02] ------------------------------------- -118: [10:23:02] Test MMFF atom types. -118: [10:23:02] done -118: [10:23:02] ------------------------------------- -118: [10:23:02] Testing MMFF builder tools. -118: [10:23:02] done -118: [10:23:02] ------------------------------------- -118: [10:23:02] Testing MMFF builder+minimization. -118: [10:23:03] done -118: [10:23:03] ------------------------------------- -118: [10:23:03] Testing Issue239. -118: [10:23:03] done -118: [10:23:03] ------------------------------------- -118: [10:23:03] Testing calcEnergy with passed coords. -118: [10:23:03] done -118: [10:23:03] ------------------------------------- -118: [10:23:03] Testing calcGrad. -118: [10:23:03] done -118: [10:23:03] ------------------------------------- -118: [10:23:03] Testing Issue242. -118: [10:23:03] done -118: [10:23:03] ------------------------------------- -118: [10:23:03] Testing github 308: crash during MMFF parameterization . -118: [10:23:03] ------------------------------------- -118: [10:23:03] Testing SFIssue1653802. -118: [10:23:03] done -118: [10:23:03] ------------------------------------- -118: [10:23:03] Testing SFIssue2378119. -118: [10:23:03] done -118: [10:23:03] ------------------------------------- -118: [10:23:03] Test MMFF force-field parameter getters. -118: [10:23:03] ------------------------------------- -118: [10:23:03] Test MMFF multithreading +118: [18:25:52] ------------------------------------- +118: [18:25:52] Test MMFF atom types. +118: [18:25:52] done +118: [18:25:52] ------------------------------------- +118: [18:25:52] Testing MMFF builder tools. +118: [18:25:53] done +118: [18:25:53] ------------------------------------- +118: [18:25:53] Testing MMFF builder+minimization. +118: [18:25:53] done +118: [18:25:53] ------------------------------------- +118: [18:25:53] Testing Issue239. +118: [18:25:54] done +118: [18:25:54] ------------------------------------- +118: [18:25:54] Testing calcEnergy with passed coords. +118: [18:25:54] done +118: [18:25:54] ------------------------------------- +118: [18:25:54] Testing calcGrad. +118: [18:25:54] done +118: [18:25:54] ------------------------------------- +118: [18:25:54] Testing Issue242. +118: [18:25:55] done +118: [18:25:55] ------------------------------------- +118: [18:25:55] Testing github 308: crash during MMFF parameterization . +118: [18:25:55] ------------------------------------- +118: [18:25:55] Testing SFIssue1653802. +118: [18:25:55] done +118: [18:25:55] ------------------------------------- +118: [18:25:55] Testing SFIssue2378119. +118: [18:25:55] done +118: [18:25:55] ------------------------------------- +118: [18:25:55] Test MMFF force-field parameter getters. +118: [18:25:55] ------------------------------------- +118: [18:25:55] Test MMFF multithreading 118: generating reference data 118: processing 118: launch :0 118: launch :1 118: launch :2 118: launch :3 -118: [10:23:06] Rep: 0 Mol:0 -118: [10:23:06] Rep: 0 Mol:[10:23:06] Rep: 0 Mol:2 -118: [10:23:06] Rep: 0 Mol:3 -118: 1 -118: [10:23:06] Rep: 0 Mol:5 -118: [10:23:06] Rep: 0 Mol:9 -118: [10:23:06] Rep: 0 Mol:4 -118: [10:23:06] Rep: 0 Mol:13 -118: [10:23:06] Rep: 0 Mol:6 -118: [10:23:06] Rep: 0 Mol:17 -118: [10:23:06] Rep: 0 Mol:10 -118: [10:23:07] Rep: 0 Mol:8 -118: [10:23:07] Rep: 0 Mol:7 -118: [10:23:07] Rep: 0 Mol:12 -118: [10:23:07] Rep: 0 Mol:11 -118: [10:23:07] Rep: 0 Mol:16 -118: [10:23:07] Rep: 0 Mol:21 -118: [10:23:07] Rep: 0 Mol:15 -118: [10:23:07] Rep: 0 Mol:19 -118: [10:23:07] Rep: 0 Mol:25 -118: [10:23:07] Rep: 0 Mol:23 -118: [10:23:07] Rep: 0 Mol:27 -118: [10:23:07] Rep: 0 Mol:20 -118: [10:23:07] Rep: 0 Mol:31 -118: [10:23:07] Rep: 0 Mol:29 -118: [10:23:07] Rep: 0 Mol:24 -118: [10:23:07] Rep: 0 Mol:14 -118: [10:23:07] Rep: 0 Mol:28 -118: [10:23:07] Rep: 0 Mol:18 -118: [10:23:07] Rep: 0 Mol:22 -118: [10:23:07] Rep: 0 Mol:26 -118: [10:23:07] Rep: 0 Mol:30 -118: [10:23:08] Rep: 20 Mol:3 -118: [10:23:08] Rep: 20 Mol:7 -118: [10:23:08] Rep: 20 Mol:11 -118: [10:23:08] Rep: 20 Mol:15 -118: [10:23:08] Rep: 20 Mol:19 -118: [10:23:08] Rep: 20 Mol:23 -118: [10:23:08] Rep: 20 Mol:27 -118: [10:23:08] Rep: 20 Mol:31 -118: [10:23:08] Rep: 20 Mol:1 -118: [10:23:08] Rep: 20 Mol:5 -118: [10:23:08] Rep: 20 Mol:9 -118: [10:23:08] Rep: 20 Mol:13 -118: [10:23:08] Rep: 20 Mol:17 -118: [10:23:08] Rep: 20 Mol:21 -118: [10:23:08] Rep: 20 Mol:25 -118: [10:23:08] Rep: 20 Mol:29 -118: [10:23:08] Rep: 20 Mol:0 -118: [10:23:08] Rep: 20 Mol:4 -118: [10:23:08] Rep: 20 Mol:8 -118: [10:23:08] Rep: 20 Mol:12 -118: [10:23:08] Rep: 20 Mol:16 -118: [10:23:08] Rep: 20 Mol:20 -118: [10:23:08] Rep: 20 Mol:24 -118: [10:23:08] Rep: 20 Mol:28 -118: [10:23:09] Rep: 40 Mol:3 -118: [10:23:09] Rep: 40 Mol:7 -118: [10:23:09] Rep: 40 Mol:11 -118: [10:23:09] Rep: 40 Mol:15 -118: [10:23:09] Rep: 40 Mol:19 -118: [10:23:09] Rep: 40 Mol:23 -118: [10:23:09] Rep: 40 Mol:27 -118: [10:23:09] Rep: 40 Mol:31 -118: [10:23:09] Rep: 40 Mol:1 -118: [10:23:09] Rep: 40 Mol:5 -118: [10:23:09] Rep: 20 Mol:2 -118: [10:23:09] Rep: 40 Mol:9 -118: [10:23:09] Rep: 40 Mol:13 -118: [10:23:09] Rep: 40 Mol:17 -118: [10:23:09] Rep: 20 Mol:6 -118: [10:23:09] Rep: 20 Mol:10 -118: [10:23:09] Rep: 40 Mol:21 -118: [10:23:09] Rep: 40 Mol:25 -118: [10:23:09] Rep: 40 Mol:29 -118: [10:23:09] Rep: 20 Mol:14 -118: [10:23:09] Rep: 20 Mol:18 -118: [10:23:09] Rep: 20 Mol:22 -118: [10:23:09] Rep: 20 Mol:26 -118: [10:23:09] Rep: 20 Mol:30 -118: [10:23:09] Rep: 40 Mol:0 -118: [10:23:09] Rep: 40 Mol:4 -118: [10:23:09] Rep: 40 Mol:8 -118: [10:23:09] Rep: 40 Mol:12 -118: [10:23:09] Rep: 40 Mol:16 -118: [10:23:09] Rep: 40 Mol:20 -118: [10:23:09] Rep: 40 Mol:24 -118: [10:23:09] Rep: 40 Mol:28 -118: [10:23:09] Rep: 60 Mol:3 -118: [10:23:09] Rep: 60 Mol:7 -118: [10:23:09] Rep: 60 Mol:11 -118: [10:23:09] Rep: 60 Mol:15 -118: [10:23:09] Rep: 60 Mol:19 -118: [10:23:09] Rep: 60 Mol:23 -118: [10:23:09] Rep: 60 Mol:27 -118: [10:23:09] Rep: 60 Mol:31 -118: [10:23:10] Rep: 80 Mol:3 -118: [10:23:10] Rep: 80 Mol:7 -118: [10:23:10] Rep: 80 Mol:11 -118: [10:23:10] Rep: 80 Mol:15 -118: [10:23:10] Rep: 80 Mol:19 -118: [10:23:10] Rep: 80 Mol:23 -118: [10:23:10] Rep: 80 Mol:27 -118: [10:23:10] Rep: 80 Mol:31 -118: [10:23:10] Rep: 60 Mol:1 -118: [10:23:10] Rep: 60 Mol:5 -118: [10:23:10] Rep: 60 Mol:9 -118: [10:23:10] Rep: 60 Mol:13 -118: [10:23:10] Rep: 60 Mol:17 -118: [10:23:10] Rep: 60 Mol:21 -118: [10:23:10] Rep: 60 Mol:25 -118: [10:23:10] Rep: 60 Mol:29 -118: [10:23:10] Rep: 40 Mol:2 -118: [10:23:10] Rep: 40 Mol:6 -118: [10:23:10] Rep: 40 Mol:10 -118: [10:23:10] Rep: 40 Mol:14 -118: [10:23:10] Rep: 40 Mol:18 -118: [10:23:10] Rep: 40 Mol:22 -118: [10:23:10] Rep: 60 Mol:0 -118: [10:23:10] Rep: 60 Mol:4 -118: [10:23:10] Rep: 40 Mol:26 -118: [10:23:10] Rep: 40 Mol:30 -118: [10:23:10] Rep: 60 Mol:8 -118: [10:23:10] Rep: 60 Mol:12 -118: [10:23:10] Rep: 60 Mol:16 -118: [10:23:10] Rep: 60 Mol:20 -118: [10:23:10] Rep: 60 Mol:24 -118: [10:23:10] Rep: 60 Mol:28 -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -108: [10:23:11] Warning: molecule is tagged as 3D, but all Z coords are zero -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Test unfolded version of RDKFP -108: [10:23:11] ------------------------------------- -108: [10:23:11] Test bitinfo of RDKFP -108: [10:23:11] ------------------------------------- -108: [10:23:11] Single atoms setting radius 1 bits in Morgan fingerprints -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Github #879: Pattern fingerprint should set bits for single-atom fragments. -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Github #2115: BitInfo not complete for RDKFingerprint -108: [10:23:11] done -108: [10:23:11] ------------------------------------- -108: [10:23:11] Github #3723: Fingerprint crash for mols with Zero order bonds -116/208 Test #108: testFingerprints ....................... Passed 22.27 sec +118: [18:25:59] Rep: 0 Mol:3 +118: [18:25:59] Rep: 0 Mol:2 +118: [18:25:59] Rep: 0 Mol:0 +118: [18:25:59] Rep: 0 Mol:1 +118: [18:25:59] Rep: 0 Mol:5 +118: [18:25:59] Rep: 0 Mol:9 +118: [18:25:59] Rep: 0 Mol:4 +118: [18:25:59] Rep: 0 Mol:13 +118: [18:26:00] Rep: 0 Mol:6 +118: [18:26:00] Rep: 0 Mol:10 +118: [18:26:00] Rep: 0 Mol:17 +118: [18:26:00] Rep: 0 Mol:8 +118: [18:26:00] Rep: 0 Mol:7 +118: [18:26:00] Rep: 0 Mol:11 +118: [18:26:00] Rep: 0 Mol:15 +118: [18:26:00] Rep: 0 Mol:12 +118: [18:26:00] Rep: 0 Mol:19 +118: [18:26:00] Rep: 0 Mol:16 +118: [18:26:00] Rep: 0 Mol:23 +118: [18:26:00] Rep: 0 Mol:27 +118: [18:26:00] Rep: 0 Mol:31 +118: [18:26:00] Rep: 0 Mol:21 +118: [18:26:00] Rep: 0 Mol:20 +118: [18:26:00] Rep: 0 Mol:25 +118: [18:26:00] Rep: 0 Mol:24 +118: [18:26:00] Rep: 0 Mol:29 +118: [18:26:00] Rep: 0 Mol:28 +118: [18:26:00] Rep: 0 Mol:14 +118: [18:26:00] Rep: 0 Mol:18 +118: [18:26:01] Rep: 0 Mol:22 +118: [18:26:01] Rep: 0 Mol:26 +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +118: [18:26:01] Rep: 0 Mol:30 +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +108: [18:26:01] Warning: molecule is tagged as 3D, but all Z coords are zero +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Test unfolded version of RDKFP +108: [18:26:01] ------------------------------------- +108: [18:26:01] Test bitinfo of RDKFP +108: [18:26:01] ------------------------------------- +108: [18:26:01] Single atoms setting radius 1 bits in Morgan fingerprints +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Github #879: Pattern fingerprint should set bits for single-atom fragments. +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Github #2115: BitInfo not complete for RDKFingerprint +108: [18:26:01] done +108: [18:26:01] ------------------------------------- +108: [18:26:01] Github #3723: Fingerprint crash for mols with Zero order bonds +115/208 Test #108: testFingerprints ....................... Passed 38.83 sec test 119 Start 119: testMMFFForceFieldHelpersMultiThread 119: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 119: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF 119: Test timeout computed to be: 1500 -119: [10:23:11] ------------------------------------- -119: [10:23:11] Test MMFF multithreading -118: [10:23:11] Rep: 80 Mol:1 -118: [10:23:11] Rep: 80 Mol:5 -118: [10:23:11] Rep: 80 Mol:9 -118: [10:23:11] Rep: 80 Mol:13 -118: [10:23:11] Rep: 80 Mol:17 -118: [10:23:11] Rep: 80 Mol:21 -118: [10:23:11] Rep: 80 Mol:25 -118: [10:23:11] Rep: 80 Mol:29 +119: [18:26:01] ------------------------------------- +119: [18:26:01] Test MMFF multithreading +118: [18:26:01] Rep: 20 Mol:3 +118: [18:26:01] Rep: 20 Mol:7 +118: [18:26:01] Rep: 20 Mol:11 +118: [18:26:01] Rep: 20 Mol:15 +118: [18:26:01] Rep: 20 Mol:19 +118: [18:26:01] Rep: 20 Mol:23 +118: [18:26:01] Rep: 20 Mol:27 +118: [18:26:01] Rep: 20 Mol:31 119: processing 119: launch :0 119: launch :1 @@ -33487,171 +33423,270 @@ 119: launch :21 119: launch :22 119: launch :23 -118: [10:23:11] Rep: 60 Mol:2 -118: [10:23:11] Rep: 60 Mol:6 -118: [10:23:11] Rep: 60 Mol:10 -118: [10:23:11] Rep: 60 Mol:14 -118: [10:23:11] Rep: 60 Mol:18 -118: [10:23:11] Rep: 60 Mol:22 -118: [10:23:11] Rep: 60 Mol:26 -118: [10:23:11] Rep: 80 Mol:0 -118: [10:23:11] Rep: 80 Mol:4 -118: [10:23:11] Rep: 60 Mol:30 -118: [10:23:11] Rep: 80 Mol:8 -118: [10:23:11] Rep: 80 Mol:12 -118: [10:23:11] Rep: 80 Mol:16 -118: [10:23:11] Rep: 80 Mol:20 -118: [10:23:11] Rep: 80 Mol:24 -118: [10:23:11] Rep: 80 Mol:28 +118: [18:26:02] Rep: 20 Mol:0 +118: [18:26:02] Rep: 20 Mol:4 +118: [18:26:02] Rep: 20 Mol:8 +118: [18:26:02] Rep: 20 Mol:12 +118: [18:26:02] Rep: 20 Mol:16 +118: [18:26:02] Rep: 20 Mol:20 +118: [18:26:02] Rep: 20 Mol:24 +118: [18:26:02] Rep: 20 Mol:28 +118: [18:26:02] Rep: 20 Mol:1 +118: [18:26:02] Rep: 20 Mol:5 +118: [18:26:02] Rep: 20 Mol:9 +118: [18:26:02] Rep: 20 Mol:13 +118: [18:26:02] Rep: 20 Mol:17 +118: [18:26:02] Rep: 20 Mol:21 +118: [18:26:02] Rep: 20 Mol:25 +118: [18:26:02] Rep: 20 Mol:29 119: done -119: [10:23:12] done -117/208 Test #119: testMMFFForceFieldHelpersMultiThread ... Passed 1.72 sec +118: [18:26:03] Rep: 40 Mol:3 +118: [18:26:03] Rep: 40 Mol:7 +118: [18:26:03] Rep: 40 Mol:11 +118: [18:26:03] Rep: 40 Mol:15 +118: [18:26:03] Rep: 40 Mol:19 +118: [18:26:03] Rep: 40 Mol:23 +118: [18:26:03] Rep: 40 Mol:27 +118: [18:26:03] Rep: 40 Mol:31 +119: [18:26:03] done +116/208 Test #119: testMMFFForceFieldHelpersMultiThread ... Passed 2.58 sec test 120 Start 120: testUFFForceFieldHelpers 120: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 120: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF 120: Test timeout computed to be: 1500 -118: [10:23:12] Rep: 80 Mol:2 -118: [10:23:12] Rep: 80 Mol:6 -118: [10:23:12] Rep: 80 Mol:10 -118: [10:23:12] Rep: 80 Mol:14 -118: [10:23:12] Rep: 80 Mol:18 -118: [10:23:12] Rep: 80 Mol:22 -118: [10:23:12] Rep: 80 Mol:26 -118: [10:23:12] Rep: 80 Mol:30 -120: [10:23:12] ------------------------------------- -120: [10:23:12] Test UFF atom labels. -120: [10:23:12] done -120: [10:23:12] ------------------------------------- -120: [10:23:12] Test UFF atom typer. -120: [10:23:12] done -120: [10:23:12] ------------------------------------- -120: [10:23:12] Testing UFF builder tools. -120: [10:23:12] done -120: [10:23:12] ------------------------------------- -120: [10:23:12] Testing UFF builder+minimization. -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Testing UFF special cases. -120: [10:23:13] UFFTYPER: Unrecognized charge state for atom: 0 -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Testing Issue239. -118: [10:23:13] done -118: [10:23:13] ------------------------------------- -118: [10:23:13] Test MMFF multithreading2 -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Testing calcEnergy with passed coords. -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Testing calcGrad. -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Testing SFIssue1653802. -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Testing SFIssue2378119. -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Test UFF force-field parameter getters. -120: [10:23:13] ------------------------------------- -120: [10:23:13] Testing handling missing parameters. -120: [10:23:13] UFFTYPER: Unrecognized hybridization for atom: 0 -120: [10:23:13] UFFTYPER: Unrecognized atom type: Cu+1 (0) -120: [10:23:13] UFFTYPER: Unrecognized hybridization for atom: 0 -120: [10:23:13] UFFTYPER: Unrecognized atom type: Cu+1 (0) -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Testing SFIssue3009337. -120: [10:23:13] done -120: [10:23:13] ------------------------------------- -120: [10:23:13] Test UFF multithreading +120: [18:26:04] ------------------------------------- +120: [18:26:04] Test UFF atom labels. +118: [18:26:04] Rep: 40 Mol:1 +118: [18:26:04] Rep: 40 Mol:5 +118: [18:26:04] Rep: 40 Mol:9 +118: [18:26:04] Rep: 40 Mol:13 +120: [18:26:04] done +120: [18:26:04] ------------------------------------- +120: [18:26:04] Test UFF atom typer. +118: [18:26:04] Rep: 40 Mol:17 +118: [18:26:04] Rep: 40 Mol:21 +118: [18:26:04] Rep: 40 Mol:25 +118: [18:26:04] Rep: 20 Mol:2 +118: [18:26:04] Rep: 20 Mol:6 +120: [18:26:04] done +120: [18:26:04] ------------------------------------- +120: [18:26:04] Testing UFF builder tools. +120: [18:26:04] done +120: [18:26:04] ------------------------------------- +120: [18:26:04] Testing UFF builder+minimization. +118: [18:26:04] Rep: 40 Mol:29 +118: [18:26:04] Rep: 20 Mol:10 +118: [18:26:04] Rep: 20 Mol:14 +118: [18:26:04] Rep: 20 Mol:18 +118: [18:26:04] Rep: 20 Mol:22 +118: [18:26:04] Rep: 20 Mol:26 +118: [18:26:04] Rep: 20 Mol:30 +118: [18:26:04] Rep: 40 Mol:0 +118: [18:26:04] Rep: 40 Mol:4 +118: [18:26:04] Rep: 40 Mol:8 +118: [18:26:04] Rep: 40 Mol:12 +118: [18:26:04] Rep: 40 Mol:16 +118: [18:26:04] Rep: 40 Mol:20 +118: [18:26:04] Rep: 40 Mol:24 +118: [18:26:04] Rep: 40 Mol:28 +118: [18:26:05] Rep: 60 Mol:3 +118: [18:26:05] Rep: 60 Mol:7 +118: [18:26:05] Rep: 60 Mol:11 +118: [18:26:05] Rep: 60 Mol:15 +118: [18:26:05] Rep: 60 Mol:19 +118: [18:26:05] Rep: 60 Mol:23 +118: [18:26:05] Rep: 60 Mol:27 +118: [18:26:05] Rep: 60 Mol:31 +120: [18:26:05] done +120: [18:26:05] ------------------------------------- +120: [18:26:05] Testing UFF special cases. +120: [18:26:05] UFFTYPER: Unrecognized charge state for atom: 0 +120: [18:26:05] done +120: [18:26:05] ------------------------------------- +120: [18:26:05] Testing Issue239. +120: [18:26:05] done +120: [18:26:05] ------------------------------------- +120: [18:26:05] Testing calcEnergy with passed coords. +120: [18:26:05] done +120: [18:26:05] ------------------------------------- +120: [18:26:05] Testing calcGrad. +118: [18:26:05] Rep: 60 Mol:1 +118: [18:26:05] Rep: 60 Mol:5 +118: [18:26:05] Rep: 60 Mol:9 +118: [18:26:05] Rep: 60 Mol:13 +118: [18:26:06] Rep: 60 Mol:17 +118: [18:26:06] Rep: 60 Mol:21 +118: [18:26:06] Rep: 60 Mol:25 +118: [18:26:06] Rep: 60 Mol:29 +120: [18:26:06] done +120: [18:26:06] ------------------------------------- +120: [18:26:06] Testing SFIssue1653802. +120: [18:26:06] done +120: [18:26:06] ------------------------------------- +120: [18:26:06] Testing SFIssue2378119. +120: [18:26:06] done +120: [18:26:06] ------------------------------------- +120: [18:26:06] Test UFF force-field parameter getters. +120: [18:26:06] ------------------------------------- +120: [18:26:06] Testing handling missing parameters. +120: [18:26:06] UFFTYPER: Unrecognized hybridization for atom: 0 +120: [18:26:06] UFFTYPER: Unrecognized atom type: Cu+1 (0) +120: [18:26:06] UFFTYPER: Unrecognized hybridization for atom: 0 +120: [18:26:06] UFFTYPER: Unrecognized atom type: Cu+1 (0) +120: [18:26:06] done +120: [18:26:06] ------------------------------------- +120: [18:26:06] Testing SFIssue3009337. +120: [18:26:06] done +120: [18:26:06] ------------------------------------- +120: [18:26:06] Test UFF multithreading 120: generating reference data +118: [18:26:06] Rep: 60 Mol:0 +118: [18:26:06] Rep: 60 Mol:4 +118: [18:26:06] Rep: 40 Mol:2 +118: [18:26:06] Rep: 40 Mol:6 +118: [18:26:06] Rep: 60 Mol:8 +118: [18:26:06] Rep: 60 Mol:12 +118: [18:26:06] Rep: 60 Mol:16 +118: [18:26:06] Rep: 60 Mol:20 +118: [18:26:06] [18:26:06] Rep: 40 Mol:10 +118: Rep: 60 Mol:24 +118: [18:26:06] Rep: 60 Mol:28 +118: [18:26:06] Rep: 40 Mol:14 +118: [18:26:06] Rep: 40 Mol:18 +118: [18:26:06] Rep: 40 Mol:22 +118: [18:26:06] Rep: 40 Mol:26 +118: [18:26:06] Rep: 40 Mol:30 +118: [18:26:06] Rep: 80 Mol:3 +118: [18:26:06] Rep: 80 Mol:7 +118: [18:26:06] Rep: 80 Mol:11 +118: [18:26:06] Rep: 80 Mol:15 +118: [18:26:06] Rep: 80 Mol:19 +118: [18:26:06] Rep: 80 Mol:23 +118: [18:26:06] Rep: 80 Mol:27 +118: [18:26:06] Rep: 80 Mol:31 +118: [18:26:07] Rep: 80 Mol:1 +118: [18:26:07] Rep: 80 Mol:5 +118: [18:26:07] Rep: 80 Mol:9 +118: [18:26:07] Rep: 80 Mol:13 +118: [18:26:07] Rep: 80 Mol:17 +118: [18:26:07] Rep: 80 Mol:21 +118: [18:26:07] Rep: 80 Mol:25 +118: [18:26:07] Rep: 80 Mol:29 +118: [18:26:08] Rep: 80 Mol:0 +118: [18:26:08] Rep: 80 Mol:4 +118: [18:26:08] Rep: 80 Mol:8 +118: [18:26:08] Rep: 80 Mol:12 +118: [18:26:08] Rep: 80 Mol:16 +118: [18:26:08] Rep: 80 Mol:20 +118: [18:26:08] Rep: 80 Mol:24 +118: [18:26:08] Rep: 80 Mol:28 +118: [18:26:08] Rep: 60 Mol:2 +118: [18:26:08] Rep: 60 Mol:6 +118: [18:26:08] Rep: 60 Mol:10 +118: [18:26:08] Rep: 60 Mol:14 +118: [18:26:08] Rep: 60 Mol:18 +118: [18:26:08] Rep: 60 Mol:22 +118: [18:26:08] Rep: 60 Mol:26 +118: [18:26:08] Rep: 60 Mol:30 120: processing 120: launch :0 120: launch :1 120: launch :2 120: launch :3 -120: [10:23:16] Rep: 0 Mol:2 -120: [10:23:16] Rep: 0 Mol:1 -120: [10:23:16] Rep: 0 Mol:0 -120: [10:23:16] Rep: 0 Mol:3 -120: [10:23:16] Rep: 0 Mol:5 -120: [10:23:16] Rep: 0 Mol:9 -120: [10:23:16] Rep: 0 Mol:4 -120: [10:23:16] Rep: 0 Mol:13 -120: [10:23:16] Rep: 0 Mol:7 -120: [10:23:16] Rep: 0 Mol:11 -120: [10:23:16] Rep: 0 Mol:17 -120: [10:23:16] Rep: 0 Mol:6 -120: [10:23:16] Rep: 0 Mol:15 -120: [10:23:16] Rep: 0 Mol:19 -120: [10:23:16] Rep: 0 Mol:10 -120: [10:23:16] Rep: 0 Mol:23 -120: [10:23:16] Rep: 0 Mol:27 -120: [10:23:16] Rep: 0 Mol:31 -120: [10:23:16] Rep: 0 Mol:8 -120: [10:23:16] Rep: 0 Mol:12 -120: [10:23:16] Rep: 0 Mol:16 -120: [10:23:16] Rep: 0 Mol:21 -120: [10:23:16] Rep: 0 Mol:20 -120: [10:23:16] Rep: 0 Mol:25 -120: [10:23:16] Rep: 0 Mol:14 -120: [10:23:16] Rep: 0 Mol:24 -120: [10:23:16] Rep: 0 Mol:28 -120: [10:23:16] Rep: 0 Mol:18 -120: [10:23:16] Rep: 0 Mol:29 -120: [10:23:16] Rep: 0 Mol:22 -120: [10:23:16] Rep: 0 Mol:26 -120: [10:23:17] Rep: 0 Mol:30 -120: [10:23:19] Rep: 100 Mol:3 -120: [10:23:19] Rep: 100 Mol:7 -120: [10:23:19] Rep: 100 Mol:11 -120: [10:23:19] Rep: 100 Mol:15 -120: [10:23:19] Rep: 100 Mol:19 -120: [10:23:19] Rep: 100 Mol:23 -120: [10:23:19] Rep: 100 Mol:27 -120: [10:23:19] Rep: 100 Mol:31 -120: [10:23:20] Rep: 100 Mol:1 -120: [10:23:20] Rep: 100 Mol:5 -120: [10:23:20] Rep: 100 Mol:9 -120: [10:23:20] Rep: 100 Mol:13 -120: [10:23:20] Rep: 100 Mol:17 -120: [10:23:20] Rep: 100 Mol:21 -120: [10:23:20] Rep: 100 Mol:25 -120: [10:23:20] Rep: 100 Mol:29 -120: [10:23:20] Rep: 100 Mol:0 -120: [10:23:20] Rep: 100 Mol:4 -120: [10:23:20] Rep: 100 Mol:8 -120: [10:23:20] Rep: 100 Mol:12 -120: [10:23:20] Rep: 100 Mol:16 -120: [10:23:20] Rep: 100 Mol:20 -120: [10:23:20] Rep: 100 Mol:24 -120: [10:23:20] Rep: 100 Mol:28 -118: [10:23:20] done -118: [10:23:20] ------------------------------------- -118: [10:23:20] Test MMFF multithreading3 -120: [10:23:21] Rep: 100 Mol:2 -120: [10:23:21] Rep: 100 Mol:6 -120: [10:23:21] Rep: 100 Mol:10 -120: [10:23:21] Rep: 100 Mol:14 -120: [10:23:21] Rep: 100 Mol:18 -120: [10:23:21] Rep: 100 Mol:22 -120: [10:23:21] Rep: 100 Mol:26 -120: [10:23:21] Rep: 100 Mol:30 -120: [10:23:25] done -120: [10:23:25] ------------------------------------- -120: [10:23:25] Test UFF multithreading2 -118: [10:23:27] done -118: [10:23:27] ------------------------------------- -118: [10:23:27] Testing github 162: Incorrect SMILES after MMFF parameterization . -118: [10:23:27] done -118: [10:23:27] ------------------------------------- -118: [10:23:27] Testing github 224: crash during MMFF parameterization . -118: [10:23:27] done -118/208 Test #118: testMMFFForceFieldHelpers .............. Passed 25.40 sec +120: [18:26:09] Rep: 0 Mol:1 +120: [18:26:09] Rep: 0 Mol:3 +120: [18:26:09] Rep: 0 Mol:0 +120: [18:26:09] Rep: 0 Mol:2 +120: [18:26:09] Rep: 0 Mol:5 +120: [18:26:09] Rep: 0 Mol:9 +120: [18:26:09] Rep: 0 Mol:4 +120: [18:26:09] Rep: 0 Mol:13 +120: [18:26:09] Rep: 0 Mol:7 +120: [18:26:09] Rep: 0 Mol:17 +120: [18:26:09] Rep: 0 Mol:11 +120: [18:26:09] Rep: 0 Mol:15 +120: [18:26:09] Rep: 0 Mol:6 +120: [18:26:09] Rep: 0 Mol:19 +120: [18:26:09] Rep: 0 Mol:23 +120: [18:26:09] Rep: 0 Mol:27 +120: [18:26:09] Rep: 0 Mol:10 +120: [18:26:09] Rep: 0 Mol:8 +120: [18:26:09] Rep: 0 Mol:31 +120: [18:26:09] Rep: 0 Mol:21 +120: [18:26:09] Rep: 0 Mol:12 +120: [18:26:09] Rep: 0 Mol:16 +120: [18:26:09] Rep: 0 Mol:25 +120: [18:26:09] Rep: 0 Mol:20 +120: [18:26:09] Rep: 0 Mol:29 +120: [18:26:09] Rep: 0 Mol:24 +120: [18:26:09] Rep: 0 Mol:14 +120: [18:26:09] Rep: 0 Mol:28 +120: [18:26:09] Rep: 0 Mol:18 +120: [18:26:10] Rep: 0 Mol:22 +120: [18:26:10] Rep: 0 Mol:26 +120: [18:26:10] Rep: 0 Mol:30 +118: [18:26:11] Rep: 80 Mol:2 +118: [18:26:11] Rep: 80 Mol:6 +118: [18:26:11] Rep: 80 Mol:10 +118: [18:26:11] Rep: 80 Mol:14 +118: [18:26:11] Rep: 80 Mol:18 +118: [18:26:11] Rep: 80 Mol:22 +118: [18:26:11] Rep: 80 Mol:26 +118: [18:26:11] Rep: 80 Mol:30 +118: [18:26:12] done +118: [18:26:12] ------------------------------------- +118: [18:26:12] Test MMFF multithreading2 +120: [18:26:13] Rep: 100 Mol:3 +120: [18:26:13] Rep: 100 Mol:7 +120: [18:26:13] Rep: 100 Mol:11 +120: [18:26:13] Rep: 100 Mol:15 +120: [18:26:13] Rep: 100 Mol:19 +120: [18:26:13] Rep: 100 Mol:23 +120: [18:26:13] Rep: 100 Mol:27 +120: [18:26:13] Rep: 100 Mol:31 +120: [18:26:14] Rep: 100 Mol:1 +120: [18:26:14] Rep: 100 Mol:5 +120: [18:26:14] Rep: 100 Mol:9 +120: [18:26:14] Rep: 100 Mol:13 +120: [18:26:14] Rep: 100 Mol:17 +120: [18:26:14] Rep: 100 Mol:21 +120: [18:26:14] Rep: 100 Mol:25 +120: [18:26:14] Rep: 100 Mol:29 +120: [18:26:14] Rep: 100 Mol:0 +120: [18:26:14] Rep: 100 Mol:4 +120: [18:26:14] Rep: 100 Mol:8 +120: [18:26:14] Rep: 100 Mol:12 +120: [18:26:14] Rep: 100 Mol:16 +120: [18:26:14] Rep: 100 Mol:20 +120: [18:26:14] Rep: 100 Mol:24 +120: [18:26:14] Rep: 100 Mol:28 +120: [18:26:16] Rep: 100 Mol:2 +120: [18:26:16] Rep: 100 Mol:6 +120: [18:26:16] Rep: 100 Mol:10 +120: [18:26:16] Rep: 100 Mol:14 +120: [18:26:16] Rep: 100 Mol:18 +120: [18:26:16] Rep: 100 Mol:22 +120: [18:26:16] Rep: 100 Mol:26 +120: [18:26:16] Rep: 100 Mol:30 +120: [18:26:23] done +120: [18:26:23] ------------------------------------- +120: [18:26:23] Test UFF multithreading2 +118: [18:26:25] done +118: [18:26:25] ------------------------------------- +118: [18:26:25] Test MMFF multithreading3 +120: [18:26:36] done +120: [18:26:36] ------------------------------------- +120: [18:26:36] Test UFF multithreading3 +118: [18:26:37] done +118: [18:26:37] ------------------------------------- +118: [18:26:37] Testing github 162: Incorrect SMILES after MMFF parameterization . +118: [18:26:37] done +118: [18:26:37] ------------------------------------- +118: [18:26:37] Testing github 224: crash during MMFF parameterization . +118: [18:26:37] done +117/208 Test #118: testMMFFForceFieldHelpers .............. Passed 44.91 sec test 121 Start 121: testCrystalForceField @@ -33660,18 +33695,46 @@ 121: Test timeout computed to be: 1500 121: ------------------------------------- 121: Test CrystalFF torsional term. -29: [10:23:28] Finished -29: [10:23:28] ------------------------------------- -29: [10:23:28] Test github1843: RWMol.clear() should not destroy ring pointer. -29: [10:23:28] Finished -119/208 Test #29: graphmolTest1 .......................... Passed 199.89 sec +118/208 Test #121: testCrystalForceField .................. Passed 1.16 sec test 122 Start 122: pyForceFieldHelpers 122: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 122: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap 122: Test timeout computed to be: 1500 -120/208 Test #121: testCrystalForceField .................. Passed 0.58 sec +122: [18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: ..[18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:41] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:42] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:42] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:42] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:42] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:43] UFFTYPER: Unrecognized hybridization for atom: 0 +122: [18:26:43] UFFTYPER: Unrecognized atom type: Cu+1 (0) +122: .[18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: ..[18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: [18:26:43] Molecule does not have explicit Hs. Consider calling AddHs() +122: ... +122: ---------------------------------------------------------------------- +122: Ran 18 tests in 2.051s +122: +122: OK +119/208 Test #122: pyForceFieldHelpers .................... Passed 5.34 sec test 123 Start 123: testDistGeomHelpers @@ -33681,194 +33744,165 @@ 123: go 123: ------------------------------------- 123: -122: [10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: ..[10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:29] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:30] UFFTYPER: Unrecognized hybridization for atom: 0 -122: [10:23:30] UFFTYPER: Unrecognized atom type: Cu+1 (0) -122: .[10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: ..[10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: [10:23:30] Molecule does not have explicit Hs. Consider calling AddHs() -122: ... -122: ---------------------------------------------------------------------- -122: Ran 18 tests in 1.290s -122: -122: OK -121/208 Test #122: pyForceFieldHelpers .................... Passed 2.73 sec +120: [18:26:47] done +120: [18:26:47] ------------------------------------- +120: [18:26:47] Testing GitHubIssue62. +120: [18:26:47] beta-lactam 39.6387 +120: [18:26:47] cyclopropanone 174.698 +120: [18:26:47] aziridine 337.986 +120: [18:26:47] aziridinone 115.248 +120: [18:26:47] isobutene 2.48217 +120: [18:26:47] acetone 1.91788 +120: [18:26:47] cyclopentanone 10.1648 +120: [18:26:47] cyclopropene 99.4921 +120: [18:26:47] cyclobutene 41.0156 +120: [18:26:47] cyclopropane 267.236 +120: [18:26:47] gamma-lactam 15.7471 +120: [18:26:48] trans-2,3-diphenylcyclopropan-1-one 203.398 +120: [18:26:48] cis-2,3-diphenylcyclopropan-1-one 206.852 +120: [18:26:48] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +120: [18:26:48] cyclopropylidencyclobutane 218.879 +120: [18:26:48] diphenylmethylidencyclobutane 79.6139 +120: [18:26:48] done +120: [18:26:48] ------------------------------------- +120: [18:26:48] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +120: [18:26:48] done +120: [18:26:48] ------------------------------------- +120: [18:26:48] Test square planar complexes +120: [18:26:48] done +120: [18:26:48] ------------------------------------- +120: [18:26:48] Test octahedral complexes +120: [18:26:48] done +120/208 Test #120: testUFFForceFieldHelpers ............... Passed 44.86 sec test 124 Start 124: distGeomHelpersCatch 124: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 124: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers 124: Test timeout computed to be: 1500 -124: [10:23:31] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, (0, 100, 0, 0, 0, 0) -124: [10:23:31] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, (0, 0, 2.5, 0, 0, 0) -124: [10:23:31] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, (0, 0, 7, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, (0, 0, 7, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, (0, 0, 7, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, (0, 0, 7, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, (0, 0, 7, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, (0, 0, 7, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, (0, 0, 7, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, (0, 0, 7, 0, 0, 0) -124: [10:23:31] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, (-1, -0.5, -0.2, -0.3, 0, -0.3) -124: [10:23:31] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, (0, 3.6, 0, 0, 0, 0) -124: [10:23:31] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, (0, 100, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, (100, 0, 0, 0, 0, 0) -124: [10:23:31] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, (0, 0, 1, 0, 0, 0) -124: [10:23:31] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, (0, 0, 1, 0, 0, 0) -124: [10:23:31] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, (0, 0, 1, 0, 0, 0) -124: [10:23:31] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, (0, 0, 1, 0, 0, 0) -124: [10:23:31] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, (0, 10, 0, 0, 0, 0) -124: [10:23:31] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, (0, 3, 0, 0, 0, 0) -124: [10:23:31] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, (0, 3, 0, 0, 0, 0) -124: [10:23:31] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, (0, 3, 0, 0, 0, 0) -124: [10:23:31] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, (0, 3, 0, 0, 0, 0) -124: [10:23:31] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, (0, 3, 0, 0, 0, 0) -124: [10:23:31] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, (0, 3, 0, 0, 0, 0) -124: [10:23:31] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, (0, 3, 0, 0, 0, 0) -124: [10:23:31] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, (0, 3, 0, 0, 0, 0) +124: [18:26:49] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, (0, 100, 0, 0, 0, 0) +124: [18:26:49] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, (0, 0, 2.5, 0, 0, 0) +124: [18:26:49] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, (0, 0, 7, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, (0, 0, 7, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, (0, 0, 7, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, (0, 0, 7, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, (0, 0, 7, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, (0, 0, 7, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, (0, 0, 7, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, (0, 0, 7, 0, 0, 0) +124: [18:26:49] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, (-1, -0.5, -0.2, -0.3, 0, -0.3) +124: [18:26:49] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, (0, 3.6, 0, 0, 0, 0) +124: [18:26:49] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, (0, 100, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, (100, 0, 0, 0, 0, 0) +124: [18:26:49] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, (0, 0, 1, 0, 0, 0) +124: [18:26:49] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, (0, 0, 1, 0, 0, 0) +124: [18:26:49] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, (0, 0, 1, 0, 0, 0) +124: [18:26:49] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, (0, 0, 1, 0, 0, 0) +124: [18:26:49] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, (0, 10, 0, 0, 0, 0) +124: [18:26:49] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, (0, 3, 0, 0, 0, 0) +124: [18:26:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, (0, 3, 0, 0, 0, 0) +124: [18:26:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, (0, 3, 0, 0, 0, 0) +124: [18:26:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, (0, 3, 0, 0, 0, 0) +124: [18:26:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, (0, 3, 0, 0, 0, 0) +124: [18:26:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, (0, 3, 0, 0, 0, 0) +124: [18:26:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, (0, 3, 0, 0, 0, 0) +124: [18:26:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, (0, 3, 0, 0, 0, 0) 124: ----------- -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, (100, 0, 0, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, (100, 0, 0, 0, 0, 0) -124: [10:23:31] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, (0, 10, 0, 0, 0, 0) -124: [10:23:31] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, (0, 10, 0, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, (0, 0, 1, 0, 0, 0) -124: [10:23:31] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, (0, 0, 1, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, (100, 0, 0, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, (100, 0, 0, 0, 0, 0) +124: [18:26:49] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, (0, 10, 0, 0, 0, 0) +124: [18:26:49] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, (0, 10, 0, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, (0, 0, 1, 0, 0, 0) +124: [18:26:49] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, (0, 0, 1, 0, 0, 0) 124: ----------- -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, (0, 0, 4, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, (100, 0, 0, 0, 0, 0) -124: [10:23:31] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, (0, 10, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, (0, 0, 4, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, (100, 0, 0, 0, 0, 0) +124: [18:26:49] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, (0, 10, 0, 0, 0, 0) 124: ----------- 124: ----------- -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, (0, 8, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, (5, 0, 0, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, (0, 0, 2, 0, 0, 0) -124: [10:23:31] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, (0, 0, 2, 0, 0, 0) -124: [10:23:31] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -124: [10:23:31] UFFTYPER: Unrecognized atom type: N_5 (2) -124: [10:23:31] UFFTYPER: Unrecognized atom type: N_5 (3) -124: [10:23:31] UFFTYPER: Unrecognized atom type: N_5 (2) -124: [10:23:31] UFFTYPER: Unrecognized atom type: N_5 (3) -124: [10:23:31] UFFTYPER: Unrecognized charge state for atom: 1 -124: [10:23:31] UFFTYPER: Unrecognized charge state for atom: 1 -124: [10:23:31] UFFTYPER: Unrecognized charge state for atom: 1 -124: [10:23:32] UFFTYPER: Unrecognized charge state for atom: 5 -124: [10:23:32] UFFTYPER: Unrecognized charge state for atom: 5 -124: [10:23:32] UFFTYPER: Unrecognized charge state for atom: 5 -120: [10:23:32] done -120: [10:23:32] ------------------------------------- -120: [10:23:32] Test UFF multithreading3 -124: [10:23:32] UFFTYPER: Unrecognized charge state for atom: 6 -124: [10:23:32] UFFTYPER: Unrecognized charge state for atom: 6 -124: [10:23:32] UFFTYPER: Unrecognized charge state for atom: 6 -120: [10:23:39] done -120: [10:23:39] ------------------------------------- -120: [10:23:39] Testing GitHubIssue62. -120: [10:23:39] beta-lactam 39.6387 -120: [10:23:39] cyclopropanone 174.698 -120: [10:23:39] aziridine 337.986 -120: [10:23:39] aziridinone 115.248 -124: [10:23:39] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -120: [10:23:39] isobutene 2.48217 -120: [10:23:39] acetone 1.91788 -120: [10:23:39] cyclopentanone 10.1648 -120: [10:23:39] cyclopropene 99.4921 -120: [10:23:39] cyclobutene 41.0156 -120: [10:23:39] cyclopropane 267.236 -120: [10:23:39] gamma-lactam 15.7471 -120: [10:23:39] trans-2,3-diphenylcyclopropan-1-one 203.398 -124: [10:23:39] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -120: [10:23:39] cis-2,3-diphenylcyclopropan-1-one 206.852 -120: [10:23:39] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -120: [10:23:39] cyclopropylidencyclobutane 218.879 -124: [10:23:39] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -120: [10:23:39] diphenylmethylidencyclobutane 79.6139 -120: [10:23:39] done -120: [10:23:39] ------------------------------------- -120: [10:23:39] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -120: [10:23:39] done -120: [10:23:39] ------------------------------------- -120: [10:23:39] Test square planar complexes -120: [10:23:39] done -120: [10:23:39] ------------------------------------- -120: [10:23:39] Test octahedral complexes -120: [10:23:39] done -122/208 Test #120: testUFFForceFieldHelpers ............... Passed 26.92 sec +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, (0, 8, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, (5, 0, 0, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, (0, 0, 2, 0, 0, 0) +124: [18:26:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, (0, 0, 2, 0, 0, 0) +124: [18:26:50] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +124: [18:26:50] UFFTYPER: Unrecognized atom type: N_5 (2) +124: [18:26:50] UFFTYPER: Unrecognized atom type: N_5 (3) +124: [18:26:50] UFFTYPER: Unrecognized atom type: N_5 (2) +124: [18:26:50] UFFTYPER: Unrecognized atom type: N_5 (3) +124: [18:26:50] UFFTYPER: Unrecognized charge state for atom: 1 +124: [18:26:50] UFFTYPER: Unrecognized charge state for atom: 1 +124: [18:26:51] UFFTYPER: Unrecognized charge state for atom: 1 +124: [18:26:52] UFFTYPER: Unrecognized charge state for atom: 5 +124: [18:26:52] UFFTYPER: Unrecognized charge state for atom: 5 +124: [18:26:52] UFFTYPER: Unrecognized charge state for atom: 5 +124: [18:26:52] UFFTYPER: Unrecognized charge state for atom: 6 +124: [18:26:53] UFFTYPER: Unrecognized charge state for atom: 6 +124: [18:26:53] UFFTYPER: Unrecognized charge state for atom: 6 +124: [18:27:01] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +124: [18:27:02] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +124: [18:27:03] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +124: [18:27:03] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: [18:27:03] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: [18:27:03] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: =============================================================================== +124: All tests passed (163 assertions in 5 test cases) +124: +121/208 Test #124: distGeomHelpersCatch ................... Passed 15.06 sec test 125 Start 125: pyDistGeomHelpers @@ -33877,19 +33911,97 @@ 125: Test timeout computed to be: 1500 123: building molecules 123: generating reference data -124: [10:23:40] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -124: [10:23:40] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -124: [10:23:40] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -124: =============================================================================== -124: All tests passed (163 assertions in 5 test cases) -124: -123/208 Test #124: distGeomHelpersCatch ................... Passed 9.42 sec +125: .[18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: ..[18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: ..[18:27:06] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:08] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:08] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:08] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:08] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:08] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:08] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:09] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:09] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:09] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:09] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:09] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:09] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:09] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:10] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:10] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:10] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:10] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:10] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[18:27:10] Molecule does not have explicit Hs. Consider calling AddHs() +29: [18:27:11] Finished +29: [18:27:11] ------------------------------------- +29: [18:27:11] Test github1843: RWMol.clear() should not destroy ring pointer. +29: [18:27:11] Finished +122/208 Test #29: graphmolTest1 .......................... Passed 504.42 sec test 126 Start 126: testMolAlign 126: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/testMolAlign 126: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign 126: Test timeout computed to be: 1500 +125: [18:27:12] Molecule does not have explicit Hs. Consider calling AddHs() 126: *********************************************************** 126: Testing MolAlign 126: --------------------------------- @@ -33911,104 +34023,29 @@ 126: testIssue241 126: 126: *********************************************************** -124/208 Test #126: testMolAlign ........................... Passed 0.46 sec +123/208 Test #126: testMolAlign ........................... Passed 1.00 sec test 127 Start 127: testO3AAlign 127: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/testO3AAlign 127: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign 127: Test timeout computed to be: 1500 -125: .[10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: ..[10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: ..[10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:40] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:41] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:42] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:42] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:42] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:42] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:42] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:42] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[10:23:42] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:42] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:43] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:44] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:45] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:45] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:13] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:15] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:17] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:19] Molecule does not have explicit Hs. Consider calling AddHs() 123: validating reference data -125: [10:23:49] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:49] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:50] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:51] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:51] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:23:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:26] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:27] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:31] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:27:35] Molecule does not have explicit Hs. Consider calling AddHs() +123: processing +123: launch :0 +123: launch :1 +123: launch :2 +123: launch :3 127: *********************************************************** 127: Testing O3AAlign 127: --------------------------------- @@ -34039,12 +34076,7 @@ 127: testMMFFO3A multithreading 127: 127: generating reference data -123: processing -123: launch :0 -123: launch :1 -123: launch :2 -123: launch :3 -125: .[10:23:56] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[18:27:43] Molecule does not have explicit Hs. Consider calling AddHs() 127: processing 127: launch :0 127: launch :1 @@ -34062,33 +34094,33 @@ 127: launch :1 127: launch :2 127: launch :3 -125: .......[10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [10:25:59] Molecule does not have explicit Hs. Consider calling AddHs() +125: .......[18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() +125: [18:30:33] Molecule does not have explicit Hs. Consider calling AddHs() 125: . 125: ---------------------------------------------------------------------- -125: Ran 18 tests in 138.860s +125: Ran 18 tests in 207.217s 125: 125: OK -125/208 Test #125: pyDistGeomHelpers ...................... Passed 140.09 sec +124/208 Test #125: pyDistGeomHelpers ...................... Passed 210.27 sec test 128 Start 128: molAlignCatchTest @@ -34098,76 +34130,87 @@ 128: =============================================================================== 128: All tests passed (9 assertions in 1 test case) 128: -126/208 Test #128: molAlignCatchTest ...................... Passed 0.16 sec +125/208 Test #128: molAlignCatchTest ...................... Passed 0.21 sec test 129 Start 129: pyMolAlign 129: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 129: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap 129: Test timeout computed to be: 1500 +129: ............[18:32:12] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:14] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:14] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:14] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:14] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:14] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:15] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:15] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:15] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:15] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:15] Molecule does not have explicit Hs. Consider calling AddHs() 127: --------------------------------- 127: test getO3AForProbeConfs 127: 127: *********************************************************** -127/208 Test #127: testO3AAlign ........................... Passed 188.17 sec +126/208 Test #127: testO3AAlign ........................... Passed 307.32 sec test 130 Start 130: testFeatures 130: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/testFeatures 130: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures 130: Test timeout computed to be: 1500 -130: [10:26:48] ------------------------------------- -130: [10:26:48] AtomType parser testing. -130: [10:26:48] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -130: [10:26:48] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -130: [10:26:48] done -130: [10:26:48] ------------------------------------- -130: [10:26:48] FeatureDefinition parser testing. -130: [10:26:48] done -130: [10:26:48] ------------------------------------- -130: [10:26:48] Test pulling feat defs from a string. -130: [10:26:48] done -130: [10:26:48] ------------------------------------- -130: [10:26:48] FeatureDef functionality testing. -130: [10:26:49] done -130: [10:26:49] ------------------------------------- -130: [10:26:49] FeatureFactory testing. -130: [10:26:49] 1 -130: [10:26:49] 2 -130: [10:26:49] 3 -130: [10:26:49] 4 -130: [10:26:49] 5 -130: [10:26:49] 6 -130: [10:26:49] done -130: [10:26:49] ------------------------------------- -130: [10:26:49] Feature Location testing. -130: [10:26:49] done -130: [10:26:49] ------------------------------------- -130: [10:26:49] Test building a FeatureFactory from a file -130: [10:26:49] done -130: [10:26:49] ------------------------------------- -130: [10:26:49] Testing Issue 224. -130: [10:26:49] done -130: [10:26:49] ------------------------------------- -130: [10:26:49] Testing Issue 225. -130: [10:26:49] done -130: [10:26:49] ------------------------------------- -130: [10:26:49] Test Issue346 -130: [10:26:49] done -130: [10:26:49] ------------------------------------- -130: [10:26:49] Test Issue347 -130: [10:26:49] done -130: [10:26:49] ------------------------------------- -130: [10:26:49] Testing Issue 348. -130: [10:26:49] SMARTS Parse Error: syntax error while parsing: [C[C] -130: [10:26:49] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -130: [10:26:49] ------------------------------------- -130: [10:26:49] Testing Nested AtomType definitions. +130: [18:32:20] ------------------------------------- +130: [18:32:20] AtomType parser testing. +130: [18:32:20] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +130: [18:32:20] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] FeatureDefinition parser testing. +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Test pulling feat defs from a string. +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] FeatureDef functionality testing. +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] FeatureFactory testing. +130: [18:32:20] 1 +130: [18:32:20] 2 +130: [18:32:20] 3 +130: [18:32:20] 4 +130: [18:32:20] 5 +130: [18:32:20] 6 +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Feature Location testing. +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Test building a FeatureFactory from a file +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Testing Issue 224. +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Testing Issue 225. +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Test Issue346 +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Test Issue347 +130: [18:32:20] done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Testing Issue 348. +130: [18:32:20] SMARTS Parse Error: syntax error while parsing: [C[C] +130: [18:32:20] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +130: [18:32:20] ------------------------------------- +130: [18:32:20] Testing Nested AtomType definitions. 130: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -130: [10:26:49] ------------------------------------- -130: [10:26:49] Testing Github Issue #252: crash when calling getPos() with no conformer. -130: [10:26:49] expect a precondition failure message below -130: [10:26:49] +130: [18:32:20] ------------------------------------- +130: [18:32:20] Testing Github Issue #252: crash when calling getPos() with no conformer. +130: [18:32:20] expect a precondition failure message below +130: [18:32:20] 130: 130: **** 130: Pre-condition Violation @@ -34176,11 +34219,11 @@ 130: Failed Expression: dp_mol->getNumConformers() 130: **** 130: -130: [10:26:49] Done -130: [10:26:49] ------------------------------------- -130: [10:26:49] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -130: [10:26:49] done -128/208 Test #130: testFeatures ........................... Passed 0.16 sec +130: [18:32:20] Done +130: [18:32:20] ------------------------------------- +130: [18:32:20] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +130: [18:32:20] done +127/208 Test #130: testFeatures ........................... Passed 0.19 sec test 131 Start 131: pyChemicalFeatures @@ -34191,20 +34234,20 @@ 131: self.failUnless(cfac.GetNumFeatureDefs() == 2) 131: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:159: DeprecationWarning: Please use assertFalse instead. 131: self.failIf(m) -131: .[10:26:50] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[18:32:23] Molecule does not have explicit Hs. Consider calling AddHs() 131: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:48: DeprecationWarning: Please use assertRaises instead. 131: self.failUnlessRaises(IndexError, lambda: cfac.GetMolFeature(mol, 3)) -131: .[10:26:50] Molecule does not have explicit Hs. Consider calling AddHs() -131: ..[10:26:51] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[10:26:51] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[10:26:51] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -131: [10:26:51] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +131: .[18:32:23] Molecule does not have explicit Hs. Consider calling AddHs() +131: ..[18:32:24] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[18:32:24] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[18:32:24] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +131: [18:32:24] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 131: ... 131: ---------------------------------------------------------------------- -131: Ran 9 tests in 0.734s +131: Ran 9 tests in 1.246s 131: 131: OK -129/208 Test #131: pyChemicalFeatures ..................... Passed 2.56 sec +128/208 Test #131: pyChemicalFeatures ..................... Passed 4.24 sec test 132 Start 132: testShapeHelpers @@ -34223,7 +34266,7 @@ 132: testGithub4364 132: 132: *********************************************************** -130/208 Test #132: testShapeHelpers ....................... Passed 0.29 sec +129/208 Test #132: testShapeHelpers ....................... Passed 0.49 sec test 133 Start 133: pyShapeHelpers @@ -34232,18 +34275,18 @@ 133: Test timeout computed to be: 1500 133: . 133: ---------------------------------------------------------------------- -133: Ran 1 test in 0.518s +133: Ran 1 test in 1.198s 133: 133: OK 133: Testing Shape Helpers wrapper -131/208 Test #133: pyShapeHelpers ......................... Passed 2.34 sec +130/208 Test #133: pyShapeHelpers ......................... Passed 4.34 sec test 134 Start 134: testMolCatalog 134: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/testMolCatalog 134: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog 134: Test timeout computed to be: 1500 -132/208 Test #134: testMolCatalog ......................... Passed 0.22 sec +131/208 Test #134: testMolCatalog ......................... Passed 0.22 sec test 135 Start 135: pyMolCatalog @@ -34252,10 +34295,10 @@ 135: Test timeout computed to be: 1500 135: . 135: ---------------------------------------------------------------------- -135: Ran 1 test in 0.071s +135: Ran 1 test in 0.070s 135: 135: OK -133/208 Test #135: pyMolCatalog ........................... Passed 1.80 sec +132/208 Test #135: pyMolCatalog ........................... Passed 2.69 sec test 136 Start 136: moldraw2DTest1 @@ -34294,29 +34337,18 @@ 136: launch :1 136: launch :2 136: launch :3 -129: ............[10:27:00] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:01] Molecule does not have explicit Hs. Consider calling AddHs() -129: ...[10:27:21] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:21] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:21] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:21] Molecule does not have explicit Hs. Consider calling AddHs() -129: [10:27:21] Molecule does not have explicit Hs. Consider calling AddHs() +129: ...[18:32:45] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:45] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:45] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:45] Molecule does not have explicit Hs. Consider calling AddHs() +129: [18:32:45] Molecule does not have explicit Hs. Consider calling AddHs() 129: ... 129: ---------------------------------------------------------------------- -129: Ran 18 tests in 81.070s +129: Ran 18 tests in 129.224s 129: 129: OK 129: Testing MolAlign Wrappers -134/208 Test #129: pyMolAlign ............................. Passed 82.80 sec +133/208 Test #129: pyMolAlign ............................. Passed 132.65 sec test 137 Start 137: moldraw2DTestCatch @@ -34328,44 +34360,44 @@ 137: file testGithub3226_3.png gave hash 1819502787U not the expected 993799198U 137: file testPNGMetadata_1.png gave hash 2101998463U not the expected 2022143293U 137: file testPNGMetadata_2.png gave hash 3782595494U not the expected 3078435362U -137: [10:27:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:32:52] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:32:52] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-1.svg gave hash 4179827925U not the expected 799391905U -137: [10:27:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:32:52] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:32:52] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-1.png gave hash 1027508316U not the expected 1551605661U -137: [10:27:28] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:28] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:32:53] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:32:53] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-2.svg gave hash 2499980011U not the expected 2605087576U -137: [10:27:28] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:28] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:32:53] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:32:53] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-2.png gave hash 2796889239U not the expected 2979412913U -137: [10:27:28] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:28] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:32:53] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:32:53] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-3.svg gave hash 3544722771U not the expected 1015633173U -137: [10:27:28] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:28] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:32:53] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:32:53] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-3.png gave hash 330712840U not the expected 1765396301U -137: [10:27:29] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:29] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:32:53] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:32:53] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-4.svg gave hash 2804458995U not the expected 830784921U -137: [10:27:29] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:29] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:32:54] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:32:54] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-4.png gave hash 2967030530U not the expected 2989933219U 137: file testHandDrawn-5a.svg gave hash 2884622705U not the expected 2845825621U -137: [10:27:39] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:39] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:33:08] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:33:08] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-5b.svg gave hash 398482570U not the expected 476521352U -137: [10:27:39] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [10:27:39] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [18:33:08] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [18:33:08] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-5.png gave hash 4043640713U not the expected 1526220279U 137: file testBrackets-5a.svg gave hash 4068248321U not the expected 1388227932U 137: file testPositionVariation-1b.svg gave hash 919690070U not the expected 2588110577U 137: file testQueryBonds-1c.svg gave hash 1784325271U not the expected 333519907U -137: [10:27:41] unrecognized bond typefile testGithub4238_1.png gave hash 857148181U not the expected 458925131U +137: [18:33:11] unrecognized bond typefile testGithub4238_1.png gave hash 857148181U not the expected 458925131U 137: file testGithub4323_1.png gave hash 446904698U not the expected 3711520691U 137: file testGithub4323_3.png gave hash 218188912U not the expected 2300228708U -137: [10:27:43] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +137: [18:33:14] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 137: file testFlexiCanvas.2a.png gave hash 2323193993U not the expected 3618977786U 137: file testFlexiCanvas.2b.png gave hash 2716110786U not the expected 2780757414U 137: file testGithub4764.sz1.svg gave hash 500301395U not the expected 493786705U @@ -34382,13 +34414,13 @@ 137: file acs1996_2.png gave hash 318073570U not the expected 83755168U 137: file acs1996_7.svg gave hash 2718384395U not the expected 763391533U 137: file acs1996_11.svg gave hash 4001805189U not the expected 2121789178U -137: [10:27:47] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. +137: [18:33:21] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. 137: file bond_highlights_4.svg gave hash 2068128924U not the expected 4115973245U 137: file bond_highlights_8.svg gave hash 2395707233U not the expected 3826056528U 137: =============================================================================== 137: All tests passed (379 assertions in 67 test cases) 137: -135/208 Test #137: moldraw2DTestCatch ..................... Passed 25.35 sec +134/208 Test #137: moldraw2DTestCatch ..................... Passed 35.44 sec test 138 Start 138: moldraw2DRxnTest1 @@ -34409,120 +34441,35 @@ 138: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C 138: file rxn_test2_2_1.png gave hash 3926348179U not the expected 997060634U 138: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl -136: Done -136: ----------------- Test Github #781: Rendering single-atom molecules 138: file rxn_test2_2_2.png gave hash 2045440801U not the expected 2090979640U -136: Done -136: ----------------- Test 3 138: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 138: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 138: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C -136: file test3_1.png gave hash 138653240U not the expected 1578780280U 138: file rxn_test2_2_3.png gave hash 3437867479U not the expected 857100114U 138: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC -136: file test3_2.png gave hash 2252903825U not the expected 1100583374U 138: file rxn_test2_2_4.png gave hash 1982049571U not the expected 610638635U 138: Done 138: ----------------- Test 3: test reactant highlighting -136: file test3_3.png gave hash 802419933U not the expected 2405974883U -136: file test3_3.svg gave hash 220863844U not the expected 3967096277U 138: file rxn_test3_1.png gave hash 2941995435U not the expected 501226401U 138: Done 138: ----------------- Test 4: some examples from SMARTS in testing 138: draw! -136: file test3_4.png gave hash 164766785U not the expected 3523404550U -136: file test3_4.svg gave hash 2724848547U not the expected 1410409071U 138: file rxn_test4_1.png gave hash 2075251294U not the expected 805353504U -136: file test3_5.png gave hash 667377464U not the expected 411486117U 138: file rxn_test4_1.svg gave hash 3996872002U not the expected 1987969092U 138: done -136: file test3_6.png gave hash 3814422911U not the expected 2817453573U -136: file test3_7.png gave hash 3884678560U not the expected 285272009U 138: file rxn_test4_2.png gave hash 1611468997U not the expected 2842629749U -136: Done -136: ----------------- Test Github774: upside-down drawings 138: file rxn_test4_2.svg gave hash 3175821457U not the expected 946039978U 138: Done -136/208 Test #138: moldraw2DRxnTest1 ...................... Passed 2.72 sec +135/208 Test #138: moldraw2DRxnTest1 ...................... Passed 6.64 sec test 139 Start 139: pyMolDraw2D 139: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 139: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap 139: Test timeout computed to be: 1500 -136: file test774_1.png gave hash 1854972040U not the expected 930347428U -136: file test774_2.png gave hash 2429471214U not the expected 1089219024U -136: Done -136: ----------------- Test 9 (molecule legends) -136: file test9_1.svg gave hash 618149026U not the expected 3204904541U -136: Done -136: ----------------- Test Github852: Lines used to wedge bonds are too thick -136: file test852_1.png gave hash 2417987646U not the expected 4140960740U -136: file test852_2.png gave hash 245570345U not the expected 4294133823U -136: ---------------- -136: ---------------- -136: ---------------- -136: ---------------- -136: Done -136: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right -136: file test860_1.png gave hash 2024936722U not the expected 1000110983U -136: file test860_2.png gave hash 223195491U not the expected 4079976606U -136: file test860_3.png gave hash 363974217U not the expected 1675954369U -136: Done -136: ----------------- Test Github #910: ugly coordinates generated for peptide chains -136: Done -136: ----------------- Test Github #932: mistake in SVG for wedged bonds -136: Done -136: ----------------- Test Github #953: default color should not be cyan -136: Done -136: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly -136: Done -136: ----------------- Test Deuterium, Tritium -136: Done -136: ----------------- Test crossed bonds -136: Done -136: ----------------- Testing drawing a second molecule -136: Done -136: ----------------- Testing drawing a grid of molecules -136: Done -136: ----------------- Testing drawMolecules -136: Done -136: ----------------- Test JSON Configuration -136: Done -136: ----------------- Testing github 1090: escape html characters in SVG output -136: Done -136: ----------------- Testing github 1035: overflow bug in SVG color generation -136: Done -136: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes -136: Done -136: ----------------- Testing github 1322: add custom atom labels -136: Done -136: ----------------- Testing use of a black & white palette -136: Done -136: ----------------- Testing use of continuous highlighting with drawMolecules -136: Done -136: ----------------- Test 17 - Testing maximum font size -136: Done -136: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list -136: Done -136: ----------------- Testing use of fixed scales for drawing. -139: ...[10:27:53] Font file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -139: [10:27:53] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -136: Done -136: ----------------- Testing rotation of 2D drawing. -136: Done -136: ----------------- Testing inclusion of molecule metadata -136: Done -136: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default -136: Done -136: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions -136: file testGithub2151_1.svg gave hash 3327696636U not the expected 1918752877U -136: file testGithub2151_2.svg gave hash 2322775376U not the expected 1083134500U -136: Done -136: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn -136: Done -136: ----------------- Testing testGithub2931: multi-coloured molecule highlights. -139: ..........[10:27:53] +139: ...[18:33:33] Font file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +139: [18:33:33] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +139: ..........[18:33:33] 139: 139: **** 139: Pre-condition Violation @@ -34531,93 +34478,52 @@ 139: Failed Expression: m 139: **** 139: -136: Done -136: ----------------- Testing annotation of 2D Drawing. -136: file test20_1.png gave hash 3005935546U not the expected 221585048U -136: file test20_2.png gave hash 955857851U not the expected 1113799362U -136: file test20_3.png gave hash 652955779U not the expected 1764616972U -136: file test20_4.png gave hash 4274652913U not the expected 781264160U -136: Done -136: ----------------- Test 21 - different font -136: [10:27:54] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/No_Such_Font_File.ttf not found. -136: [10:27:54] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -136: Done -136: ----------------- Test 22 - draw explicit methyls. -136: Done -136: ----------------- Testing drawing of legends. -136: Done -136: ----------------- Test Github 3305 - change and scale line widths. -136: file testGithub3305_1.png gave hash 1649973233U not the expected 316930677U 139: ................... 139: ---------------------------------------------------------------------- -139: Ran 32 tests in 1.583s +139: Ran 32 tests in 3.063s 139: 139: OK -136: file testGithub3305_2.png gave hash 792521154U not the expected 3520446560U -137/208 Test #139: pyMolDraw2D ............................ Passed 3.71 sec +136/208 Test #139: pyMolDraw2D ............................ Passed 7.26 sec test 140 Start 140: testFMCS 140: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/testFMCS 140: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS 140: Test timeout computed to be: 1500 -136: file testGithub3305_3.png gave hash 2523307617U not the expected 3960184199U -136: file testGithub3305_4.png gave hash 667377464U not the expected 411486117U -136: file testGithub3305_5.png gave hash 3248064742U not the expected 3988290371U -136: file testGithub3305_6.png gave hash 3441116188U not the expected 4125772769U -136: file testGithub3305_7.png gave hash 2685906518U not the expected 972161580U -136: Done -136: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. -136: Done -136: ----------------- Test Github 4156 - bad scale for radicals in grid -136: Done -136: ----------------- Test JSON atomColourPalette -136: Done -136: ----------------- Test draw aromatic OR queries -136: Done -136: ----------------- Test AND queries -136: Done -138/208 Test #136: moldraw2DTest1 ......................... Passed 59.04 sec -test 141 - Start 141: pyFMCS - -141: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" -141: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap -141: Test timeout computed to be: 1500 140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 140: Time elapsed 0.001 seconds 140: 140: test32() 140: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds -140: Time elapsed 0.504 seconds +140: Time elapsed 0.866 seconds 140: 140: test190() 140: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds -140: Time elapsed 0.067 seconds +140: Time elapsed 0.107 seconds 140: 140: test3() 140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -140: Time elapsed 0.119 seconds +140: Time elapsed 0.183 seconds 140: 140: testSimpleFast() 140: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds -140: Time elapsed 0.876 seconds +140: Time elapsed 1.373 seconds 140: 140: testSimple() 140: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -140: Time elapsed 0.929 seconds +140: Time elapsed 1.100 seconds 140: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -140: Time elapsed 0.917 seconds +140: Time elapsed 1.368 seconds 140: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -140: Time elapsed 1.003 seconds +140: Time elapsed 1.426 seconds 140: 140: testSegFault() 140: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.064 seconds +140: Time elapsed 0.098 seconds 140: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.079 seconds +140: Time elapsed 0.118 seconds 140: MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.105 seconds +140: Time elapsed 0.124 seconds 140: 140: testThreshold() 140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -34625,15 +34531,15 @@ 140: 140: testRing1() 140: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -140: Time elapsed 3.919 seconds +140: Time elapsed 5.967 seconds 140: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -140: Time elapsed 1.935 seconds +140: Time elapsed 3.852 seconds 140: MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#7]:&@[#6](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds -140: Time elapsed 1.687 seconds +140: Time elapsed 2.939 seconds 140: 140: testAtomCompareIsotopes() 140: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -140: Time elapsed 0.020 seconds +140: Time elapsed 0.083 seconds 140: 140: testAtomCompareAnyAtom() 140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds @@ -34645,35 +34551,35 @@ 140: 140: testAtomCompareAnyAtom() 140: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -140: Time elapsed 0.001 seconds +140: Time elapsed 0.000 seconds 140: 140: testAtomCompareAnyAtom() 140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -140: Time elapsed 0.001 seconds +140: Time elapsed 0.000 seconds 140: 140: testJnk1LigandsDistance() 140: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds -140: Time elapsed 0.031 seconds +140: Time elapsed 0.105 seconds 140: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds -140: Time elapsed 0.004 seconds +140: Time elapsed 0.034 seconds 140: 140: test18() 140: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 140: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds -140: Time elapsed 0.026 seconds +140: Time elapsed 0.106 seconds 140: 140: test504() 140: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 140: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds -140: Time elapsed 0.307 seconds +140: Time elapsed 1.059 seconds 140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -140: Time elapsed 0.005 seconds +140: Time elapsed 0.024 seconds 140: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds -140: Time elapsed 0.111 seconds +140: Time elapsed 0.396 seconds 140: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -140: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0055 seconds. bond[0]=6 +140: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0388 seconds. bond[0]=6 140: STATISTICS: -140: Total Growing Steps = 1, MCS found on 1 step, for 0.0055 seconds +140: Total Growing Steps = 1, MCS found on 1 step, for 0.0388 seconds 140: Initial Seeds = 1, Mismatched 0 140: Inspected Seeds = 2 140: Rejected by BestSize = 0 @@ -34692,7 +34598,7 @@ 140: HashFoundInCache= 0 140: ExactMatchCalls = 0 140: ExactMatchFound = 0 -140: Time elapsed 0.006 seconds +140: Time elapsed 0.040 seconds 140: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 140: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 140: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 @@ -34792,15 +34698,141 @@ 140: 140: MCS: [#6]-&!@[#6] 2 atoms, 1 bonds 140: -140: [10:28:14] The provided InitialSeed is not an MCS and will be ignored +136: Done +136: ----------------- Test Github #781: Rendering single-atom molecules +136: Done +136: ----------------- Test 3 +136: file test3_1.png gave hash 138653240U not the expected 1578780280U +136: file test3_2.png gave hash 2252903825U not the expected 1100583374U +136: file test3_3.png gave hash 802419933U not the expected 2405974883U +136: file test3_3.svg gave hash 220863844U not the expected 3967096277U +136: file test3_4.png gave hash 164766785U not the expected 3523404550U +136: file test3_4.svg gave hash 2724848547U not the expected 1410409071U +136: file test3_5.png gave hash 667377464U not the expected 411486117U +136: file test3_6.png gave hash 3814422911U not the expected 2817453573U +136: file test3_7.png gave hash 3884678560U not the expected 285272009U +136: Done +136: ----------------- Test Github774: upside-down drawings +136: file test774_1.png gave hash 1854972040U not the expected 930347428U +136: file test774_2.png gave hash 2429471214U not the expected 1089219024U +136: Done +136: ----------------- Test 9 (molecule legends) +136: file test9_1.svg gave hash 618149026U not the expected 3204904541U +136: Done +136: ----------------- Test Github852: Lines used to wedge bonds are too thick +136: file test852_1.png gave hash 2417987646U not the expected 4140960740U +136: file test852_2.png gave hash 245570345U not the expected 4294133823U +136: ---------------- +136: ---------------- +136: ---------------- +136: ---------------- +136: Done +136: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +136: file test860_1.png gave hash 2024936722U not the expected 1000110983U +136: file test860_2.png gave hash 223195491U not the expected 4079976606U +136: file test860_3.png gave hash 363974217U not the expected 1675954369U +136: Done +136: ----------------- Test Github #910: ugly coordinates generated for peptide chains +136: Done +136: ----------------- Test Github #932: mistake in SVG for wedged bonds +136: Done +136: ----------------- Test Github #953: default color should not be cyan +136: Done +136: ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly +136: Done +136: ----------------- Test Deuterium, Tritium +136: Done +136: ----------------- Test crossed bonds +136: Done +136: ----------------- Testing drawing a second molecule +136: Done +136: ----------------- Testing drawing a grid of molecules +136: Done +136: ----------------- Testing drawMolecules +136: Done +136: ----------------- Test JSON Configuration +136: Done +136: ----------------- Testing github 1090: escape html characters in SVG output +136: Done +136: ----------------- Testing github 1035: overflow bug in SVG color generation +136: Done +136: ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes +136: Done +136: ----------------- Testing github 1322: add custom atom labels +136: Done +136: ----------------- Testing use of a black & white palette +136: Done +136: ----------------- Testing use of continuous highlighting with drawMolecules +136: Done +136: ----------------- Test 17 - Testing maximum font size +136: Done +136: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list +136: Done +136: ----------------- Testing use of fixed scales for drawing. +136: Done +136: ----------------- Testing rotation of 2D drawing. +136: Done +136: ----------------- Testing inclusion of molecule metadata +136: Done +136: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default +136: Done +136: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions +136: file testGithub2151_1.svg gave hash 3327696636U not the expected 1918752877U +136: file testGithub2151_2.svg gave hash 2322775376U not the expected 1083134500U +136: Done +136: ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn +136: Done +136: ----------------- Testing testGithub2931: multi-coloured molecule highlights. +136: Done +136: ----------------- Testing annotation of 2D Drawing. +136: file test20_1.png gave hash 3005935546U not the expected 221585048U +136: file test20_2.png gave hash 955857851U not the expected 1113799362U +136: file test20_3.png gave hash 652955779U not the expected 1764616972U +136: file test20_4.png gave hash 4274652913U not the expected 781264160U +136: Done +136: ----------------- Test 21 - different font +136: [18:34:04] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/No_Such_Font_File.ttf not found. +136: [18:34:04] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +136: Done +136: ----------------- Test 22 - draw explicit methyls. +136: Done +136: ----------------- Testing drawing of legends. +136: Done +136: ----------------- Test Github 3305 - change and scale line widths. +136: file testGithub3305_1.png gave hash 1649973233U not the expected 316930677U +136: file testGithub3305_2.png gave hash 792521154U not the expected 3520446560U +136: file testGithub3305_3.png gave hash 2523307617U not the expected 3960184199U +136: file testGithub3305_4.png gave hash 667377464U not the expected 411486117U +136: file testGithub3305_5.png gave hash 3248064742U not the expected 3988290371U +136: file testGithub3305_6.png gave hash 3441116188U not the expected 4125772769U +136: file testGithub3305_7.png gave hash 2685906518U not the expected 972161580U +136: Done +136: ----------------- Test Github 3391 - maxFontSize interacting badly with DrawMolecules. +136: Done +136: ----------------- Test Github 4156 - bad scale for radicals in grid +136: Done +136: ----------------- Test JSON atomColourPalette +136: Done +136: ----------------- Test draw aromatic OR queries +136: Done +136: ----------------- Test AND queries +136: Done +137/208 Test #136: moldraw2DTest1 ......................... Passed 94.60 sec +test 141 + Start 141: pyFMCS + +141: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" +141: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap +141: Test timeout computed to be: 1500 +140: [18:34:13] The provided InitialSeed is not an MCS and will be ignored 140: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 140: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 140: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 140: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 140: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 140: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -140: TOTAL Time elapsed 19.77 seconds -139/208 Test #140: testFMCS ............................... Passed 19.88 sec +140: TOTAL Time elapsed 37.29 seconds +138/208 Test #140: testFMCS ............................... Passed 37.47 sec test 142 Start 142: FMCStest @@ -36772,7 +36804,7 @@ 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 142: ERROR: RDKit could not load input file -140/208 Test #142: FMCStest ............................... Passed 0.52 sec +139/208 Test #142: FMCStest ............................... Passed 0.40 sec test 143 Start 143: molHashCatchTest @@ -36782,7 +36814,7 @@ 143: =============================================================================== 143: All tests passed (60 assertions in 5 test cases) 143: -141/208 Test #143: molHashCatchTest ....................... Passed 0.27 sec +140/208 Test #143: molHashCatchTest ....................... Passed 0.33 sec test 144 Start 144: pyMolHash @@ -36791,10 +36823,10 @@ 144: Test timeout computed to be: 1500 144: .. 144: ---------------------------------------------------------------------- -144: Ran 2 tests in 0.055s +144: Ran 2 tests in 0.125s 144: 144: OK -142/208 Test #144: pyMolHash .............................. Passed 1.22 sec +141/208 Test #144: pyMolHash .............................. Passed 3.30 sec test 145 Start 145: testMMPA @@ -36803,7 +36835,7 @@ 145: Test timeout computed to be: 1500 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -145: Time elapsed 0.022085 seconds +145: Time elapsed 0.019768 seconds 145: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 145: 1: NOREF. Reference data NOT LISTED in test case. 145: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -36844,7 +36876,7 @@ 145: --- UNMATCHED Reference RESULTS: --- 145: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 145: ----------------------------------- -145: Time elapsed 0.022410 seconds +145: Time elapsed 0.031102 seconds 145: 145: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 145: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -36886,7 +36918,7 @@ 145: ----------------------------------- 145: 145: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -145: Time elapsed 0.012439 seconds +145: Time elapsed 0.023404 seconds 145: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 145: 1: PASSED. matchedRefRes = 4 145: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] @@ -36926,7 +36958,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -145: Time elapsed 0.004088 seconds +145: Time elapsed 0.001821 seconds 145: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 145: 1: PASSED. matchedRefRes = 2 145: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -36948,7 +36980,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -145: Time elapsed 0.013829 seconds +145: Time elapsed 0.043638 seconds 145: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 145: 1: NOREF. Reference data NOT LISTED in test case. 145: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -36991,7 +37023,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -145: Time elapsed 0.015020 seconds +145: Time elapsed 0.044433 seconds 145: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 145: 1: NOREF. Reference data NOT LISTED in test case. 145: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -37032,47 +37064,35 @@ 145: --- ALL PASSED --- 145: ----------------------------------- 145: 5 TEST CASES FAILED -143/208 Test #145: testMMPA ............................... Passed 0.58 sec +142/208 Test #145: testMMPA ............................... Passed 1.08 sec test 146 Start 146: pyMMPA 146: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" 146: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap 146: Test timeout computed to be: 1500 -141: ...........................................[10:28:18] The provided InitialSeed is not an MCS and will be ignored -141: [10:28:18] The provided InitialSeed is not an MCS and will be ignored -141: [10:28:18] The provided InitialSeed is not an MCS and will be ignored -141: .[10:28:18] The provided InitialSeed is not an MCS and will be ignored -141: [10:28:18] The provided InitialSeed is not an MCS and will be ignored -141: [10:28:18] The provided InitialSeed is not an MCS and will be ignored -141: .[10:28:19] The provided InitialSeed is not an MCS and will be ignored -141: [10:28:19] The provided InitialSeed is not an MCS and will be ignored -141: [10:28:19] The provided InitialSeed is not an MCS and will be ignored -141: .[10:28:19] The provided InitialSeed is not an MCS and will be ignored -141: [10:28:19] The provided InitialSeed is not an MCS and will be ignored -141: [10:28:19] The provided InitialSeed is not an MCS and will be ignored -141: ................. -141: ---------------------------------------------------------------------- -141: Ran 63 tests in 23.112s -141: -141: OK -144/208 Test #141: pyFMCS ................................. Passed 24.44 sec +146: ......... +146: ---------------------------------------------------------------------- +146: Ran 9 tests in 12.552s +146: +146: OK +143/208 Test #146: pyMMPA ................................. Passed 15.40 sec test 147 Start 147: testCIPLabeler 147: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/testCIPLabeler 147: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler 147: Test timeout computed to be: 1500 -147: [10:28:20] non kekulizable aromatic bond being treated as bond order 1 -147: [10:28:20] non kekulizable aromatic bond being treated as bond order 1 -147: [10:28:20] non kekulizable aromatic bond being treated as bond order 1 -147: [10:28:20] non kekulizable aromatic bond being treated as bond order 1 -147: [10:28:20] non kekulizable aromatic bond being treated as bond order 1 -147: [10:28:20] non kekulizable aromatic bond being treated as bond order 1 +147: [18:34:34] non kekulizable aromatic bond being treated as bond order 1 +147: [18:34:34] non kekulizable aromatic bond being treated as bond order 1 +147: [18:34:34] non kekulizable aromatic bond being treated as bond order 1 +147: [18:34:34] non kekulizable aromatic bond being treated as bond order 1 +147: [18:34:34] non kekulizable aromatic bond being treated as bond order 1 +147: [18:34:34] non kekulizable aromatic bond being treated as bond order 1 147: =============================================================================== 147: All tests passed (5974 assertions in 12 test cases) 147: -145/208 Test #147: testCIPLabeler ......................... Passed 0.26 sec +144/208 Test #147: testCIPLabeler ......................... Passed 0.40 sec test 148 Start 148: pyCIPLabelsWrapTest @@ -37081,22 +37101,34 @@ 148: Test timeout computed to be: 1500 148: ... 148: ---------------------------------------------------------------------- -148: Ran 3 tests in 0.049s +148: Ran 3 tests in 0.124s 148: 148: OK -146/208 Test #148: pyCIPLabelsWrapTest .................... Passed 1.20 sec +145/208 Test #148: pyCIPLabelsWrapTest .................... Passed 3.56 sec test 149 Start 149: pyCIPLabelsValidation 149: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 149: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap 149: Test timeout computed to be: 1500 -146: ......... -146: ---------------------------------------------------------------------- -146: Ran 9 tests in 7.016s -146: -146: OK -147/208 Test #146: pyMMPA ................................. Passed 8.30 sec +141: ...........................................[18:34:54] The provided InitialSeed is not an MCS and will be ignored +141: [18:34:54] The provided InitialSeed is not an MCS and will be ignored +141: [18:34:54] The provided InitialSeed is not an MCS and will be ignored +141: .[18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: [18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: [18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: .[18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: [18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: [18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: .[18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: [18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: [18:34:55] The provided InitialSeed is not an MCS and will be ignored +141: ................. +141: ---------------------------------------------------------------------- +141: Ran 63 tests in 46.373s +141: +141: OK +146/208 Test #141: pyFMCS ................................. Passed 49.72 sec test 150 Start 150: deprotectTest @@ -37106,7 +37138,7 @@ 150: =============================================================================== 150: All tests passed (111 assertions in 3 test cases) 150: -148/208 Test #150: deprotectTest .......................... Passed 0.56 sec +147/208 Test #150: deprotectTest .......................... Passed 0.72 sec test 151 Start 151: pyDeprotect @@ -37115,7 +37147,7 @@ 151: Test timeout computed to be: 1500 151: ..... 151: ---------------------------------------------------------------------- -151: Ran 5 tests in 0.262s +151: Ran 5 tests in 0.440s 151: 151: OK 151: Testing tert-butyldimethylsilyl @@ -37168,7 +37200,7 @@ 151: Testing acetamide 151: Testing carbobenzyloxy 151: Testing Acetal/Ketal -149/208 Test #151: pyDeprotect ............................ Passed 2.05 sec +148/208 Test #151: pyDeprotect ............................ Passed 3.03 sec test 152 Start 152: testReducedGraphs @@ -37193,7 +37225,7 @@ 152: 152: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 152: -150/208 Test #152: testReducedGraphs ...................... Passed 0.23 sec +149/208 Test #152: testReducedGraphs ...................... Passed 0.43 sec test 153 Start 153: pyReducedGraphs @@ -37202,454 +37234,454 @@ 153: Test timeout computed to be: 1500 153: ..... 153: ---------------------------------------------------------------------- -153: Ran 5 tests in 0.067s +153: Ran 5 tests in 0.184s 153: 153: OK -151/208 Test #153: pyReducedGraphs ........................ Passed 0.98 sec +150/208 Test #153: pyReducedGraphs ........................ Passed 3.10 sec test 154 Start 154: trajectoryTest 154: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/trajectoryTest 154: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory 154: Test timeout computed to be: 1500 -152/208 Test #154: trajectoryTest ......................... Passed 1.59 sec +151/208 Test #154: trajectoryTest ......................... Passed 4.48 sec test 155 Start 155: substructLibraryTest 155: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/substructLibraryTest 155: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary 155: Test timeout computed to be: 1500 -155: [10:28:30] ------------------------------------- -155: [10:28:30] Test1 -155: [10:28:31] done -155: [10:28:31] ------------------------------------- -155: [10:28:31] Test2 -155: [10:28:32] done -155: [10:28:32] ------------------------------------- -155: [10:28:32] Test3 (stereo options) -155: [10:28:32] Done (stereo options) -155: [10:28:32] ------------------------------------- -155: [10:28:32] Test4 (trusted smiles) -155: [10:28:33] Done (trusted smiles) -155: [10:28:33] ------------------------------------- -155: [10:28:33] Testing C++ docs -155: [10:28:33] Done (C++ doc tests) -155: [10:28:33] ------------------------------------- -155: [10:28:33] Testing C++ ring query: PatternHolder -155: [10:28:33] Done (C++ ring query tests) -155: [10:28:33] ------------------------------------- -155: [10:28:33] Testing C++ ring query: TautomerPatternHolder -155: [10:28:33] Done (C++ ring query tests) -155: [10:28:33] ------------------------------------- -155: [10:28:33] Add Patterns -155: [10:28:41] ------------------------------------- -155: [10:28:41] testing PatternHolder -155: [10:28:42] ------------------------------------- -155: [10:28:42] testing TautomerPatternHolder -155: [10:28:43] ------------------------------------- -155: [10:28:43] testSegFaultInHolder -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: syntax error while parsing: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:08] ------------------------------------- +155: [18:35:08] Test1 +155: [18:35:10] done +155: [18:35:10] ------------------------------------- +155: [18:35:10] Test2 +155: [18:35:12] done +155: [18:35:12] ------------------------------------- +155: [18:35:12] Test3 (stereo options) +155: [18:35:13] Done (stereo options) +155: [18:35:13] ------------------------------------- +155: [18:35:13] Test4 (trusted smiles) +155: [18:35:13] Done (trusted smiles) +155: [18:35:13] ------------------------------------- +155: [18:35:13] Testing C++ docs +155: [18:35:13] Done (C++ doc tests) +155: [18:35:13] ------------------------------------- +155: [18:35:13] Testing C++ ring query: PatternHolder +155: [18:35:13] Done (C++ ring query tests) +155: [18:35:13] ------------------------------------- +155: [18:35:13] Testing C++ ring query: TautomerPatternHolder +155: [18:35:13] Done (C++ ring query tests) +155: [18:35:13] ------------------------------------- +155: [18:35:13] Add Patterns +155: [18:35:25] ------------------------------------- +155: [18:35:25] testing PatternHolder +155: [18:35:27] ------------------------------------- +155: [18:35:27] testing TautomerPatternHolder +155: [18:35:28] ------------------------------------- +155: [18:35:28] testSegFaultInHolder +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 155: -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [10:28:43] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [10:28:43] ------------------------------------- -155: [10:28:43] Results do not depend on numThreads +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [18:35:28] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [18:35:28] ------------------------------------- +155: [18:35:28] Results do not depend on numThreads 149: VS001: PASSED 149: VS002: PASSED 149: VS003: PASSED @@ -37952,7 +37984,7 @@ 149: VS300: PASSED 149: Check finished: 0 molecules failed. 149: Failed: -153/208 Test #149: pyCIPLabelsValidation .................. Passed 35.96 sec +152/208 Test #149: pyCIPLabelsValidation .................. Passed 66.71 sec test 156 Start 156: substructLibraryCatchTest @@ -37962,32 +37994,30 @@ 156: =============================================================================== 156: All tests passed (111 assertions in 4 test cases) 156: -154/208 Test #156: substructLibraryCatchTest .............. Passed 1.01 sec +153/208 Test #156: substructLibraryCatchTest .............. Passed 1.05 sec test 157 Start 157: pySubstructLibrary 157: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 157: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap 157: Test timeout computed to be: 1500 -155: [10:29:03] ------------------------------------- -155: [10:29:03] Results do not depend on numThreads (all same) -155: [10:29:03] ------------------------------------- -155: [10:29:03] testTautomerQueries -155: [10:29:03] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -155: [10:29:03] ------------------------------------- -155: [10:29:03] github3881 recursive smarts with rings -155/208 Test #155: substructLibraryTest ................... Passed 32.69 sec +155: [18:36:07] ------------------------------------- +155: [18:36:07] Results do not depend on numThreads (all same) +155: [18:36:08] ------------------------------------- +155: [18:36:08] testTautomerQueries +155: [18:36:08] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +155: [18:36:08] ------------------------------------- +155: [18:36:08] github3881 recursive smarts with rings +154/208 Test #155: substructLibraryTest ................... Passed 59.69 sec test 158 Start 158: testRGroupDecomp 158: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 158: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition 158: Test timeout computed to be: 1500 -158: [10:29:05] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -158: [10:29:05] WARNING: not removing hydrogen atom with dummy atom neighbors -158: iterative -158: bulk -157: ......[10:29:24] +158: [18:36:12] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +158: [18:36:12] WARNING: not removing hydrogen atom with dummy atom neighbors +157: ......[18:36:26] 157: 157: **** 157: Pre-condition Violation @@ -37996,7 +38026,7 @@ 157: Failed Expression: df_init 157: **** 157: -157: [10:29:24] +157: [18:36:26] 157: 157: **** 157: Pre-condition Violation @@ -38005,12 +38035,11 @@ 157: Failed Expression: df_init 157: **** 157: -158: bulk, no symmetry -158: [10:29:28] Relabelling existing label -158: Best mapping +158: iterative +158: bulk 157: ............ 157: ---------------------------------------------------------------------- -157: Ran 18 tests in 40.408s +157: Ran 18 tests in 61.181s 157: 157: OK 157: Testing atom rings @@ -38018,35 +38047,35 @@ 157: searching atom rings 157: searching bond rings 157: done -156/208 Test #157: pySubstructLibrary ..................... Passed 42.37 sec +155/208 Test #157: pySubstructLibrary ..................... Passed 64.92 sec test 159 Start 159: testRGroupDecompInternals 159: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 159: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition 159: Test timeout computed to be: 1500 -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [10:29:40] WARNING: not removing hydrogen atom with dummy atom neighbors -157/208 Test #159: testRGroupDecompInternals .............. Passed 0.21 sec +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [18:36:51] WARNING: not removing hydrogen atom with dummy atom neighbors +156/208 Test #159: testRGroupDecompInternals .............. Passed 0.36 sec test 160 Start 160: rgroupCatchTests @@ -38056,14 +38085,22 @@ 160: =============================================================================== 160: All tests passed (142 assertions in 10 test cases) 160: -158/208 Test #160: rgroupCatchTests ....................... Passed 0.94 sec +157/208 Test #160: rgroupCatchTests ....................... Passed 1.57 sec test 161 Start 161: pyRGroupDecomposition 161: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 161: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap 161: Test timeout computed to be: 1500 -159/208 Test #158: testRGroupDecomp ....................... Passed 39.81 sec +158: bulk, no symmetry +158: [18:37:05] Relabelling existing label +158: Best mapping +161: ............... +161: ---------------------------------------------------------------------- +161: Ran 15 tests in 13.448s +161: +161: OK +158/208 Test #161: pyRGroupDecomposition .................. Passed 16.62 sec test 162 Start 162: molInterchangeTest1 @@ -38078,19 +38115,19 @@ 162: {"commonchem":{"version":10},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","cipRanks":[0,0]}]}]} 162: {"commonchem":{"version":10},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2022.09.3","values":[0.5,-0.5]}]}]} 162: {"commonchem":{"version":10},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -160/208 Test #162: molInterchangeTest1 .................... Passed 0.17 sec +159/208 Test #162: molInterchangeTest1 .................... Passed 0.27 sec test 163 Start 163: molInterchangeCatchTest 163: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/molInterchangeCatchTest 163: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange 163: Test timeout computed to be: 1500 -163: [10:29:43] unrecognized bond type set to zero while writing -163: [10:29:43] unrecognized bond type set to zero while writing +163: [18:37:10] unrecognized bond type set to zero while writing +163: [18:37:10] unrecognized bond type set to zero while writing 163: =============================================================================== 163: All tests passed (14 assertions in 1 test case) 163: -161/208 Test #163: molInterchangeCatchTest ................ Passed 0.17 sec +160/208 Test #163: molInterchangeCatchTest ................ Passed 0.21 sec test 164 Start 164: pyMolInterchange @@ -38099,31 +38136,31 @@ 164: Test timeout computed to be: 1500 164: . 164: ---------------------------------------------------------------------- -164: Ran 1 test in 0.032s +164: Ran 1 test in 0.142s 164: 164: OK -162/208 Test #164: pyMolInterchange ....................... Passed 0.91 sec +161/208 Test #164: pyMolInterchange ....................... Passed 3.49 sec test 165 Start 165: testSLNParse 165: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/testSLNParse 165: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse 165: Test timeout computed to be: 1500 -165: [10:29:44] SLN Parse Error: syntax error while parsing: CH4[I=13] -165: [10:29:44] Failed parsing SLN 'CH4[I=13]' -165: [10:29:44] SLN Parser error: Atom ID 1 appears *after* its ring closure. -165: [10:29:44] SLN Parser error: Ring closure 1 does not have a corresponding opener. -165: [10:29:44] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -165: [10:29:44] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -165: [10:29:44] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -165: [10:29:44] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -165: [10:29:44] SLN Parse Error: syntax error while parsing: CH4 fff -165: [10:29:44] Failed parsing SLN 'CH4 fff' -165: [10:29:44] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -165: [10:29:44] Failed parsing SLN 'C[charge=+1] foo' -165: [10:29:44] Query property 'is' ignored on non-query atom -165: [10:29:44] Query property 'is' ignored on non-query atom -163/208 Test #165: testSLNParse ........................... Passed 0.19 sec +165: [18:37:13] SLN Parse Error: syntax error while parsing: CH4[I=13] +165: [18:37:13] Failed parsing SLN 'CH4[I=13]' +165: [18:37:14] SLN Parser error: Atom ID 1 appears *after* its ring closure. +165: [18:37:14] SLN Parser error: Ring closure 1 does not have a corresponding opener. +165: [18:37:14] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +165: [18:37:14] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +165: [18:37:14] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +165: [18:37:14] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +165: [18:37:14] SLN Parse Error: syntax error while parsing: CH4 fff +165: [18:37:14] Failed parsing SLN 'CH4 fff' +165: [18:37:14] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +165: [18:37:14] Failed parsing SLN 'C[charge=+1] foo' +165: [18:37:14] Query property 'is' ignored on non-query atom +165: [18:37:14] Query property 'is' ignored on non-query atom +162/208 Test #165: testSLNParse ........................... Passed 0.43 sec test 166 Start 166: pySLNParse @@ -38134,52 +38171,52 @@ 166: self.failUnless(m1) 166: .. 166: ---------------------------------------------------------------------- -166: Ran 2 tests in 0.037s +166: Ran 2 tests in 0.102s 166: 166: OK -164/208 Test #166: pySLNParse ............................. Passed 0.90 sec +163/208 Test #166: pySLNParse ............................. Passed 3.44 sec test 167 Start 167: pyGraphMolWrap 167: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rough_test.py" 167: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 167: Test timeout computed to be: 1500 -167: ..............[10:29:47] SMARTS Parse Error: syntax error while parsing: fiib -167: [10:29:47] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -167: ....[10:29:47] ERROR: Problems encountered parsing data fields -167: [10:29:47] ERROR: moving to the beginning of the next molecule -167: [10:29:47] ERROR: Problems encountered parsing data fields -167: [10:29:47] ERROR: moving to the beginning of the next molecule -167: [10:29:47] Spurious data before the first property will be ignored -167: [10:29:47] Property will be truncated after the first blank line -167: [10:29:47] Property will be truncated after the first blank line -167: [10:29:47] Property will be truncated after the first blank line -167: [10:29:47] ERROR: Problems encountered parsing data fields -167: [10:29:47] ERROR: moving to the beginning of the next molecule -167: [10:29:47] ERROR: Problems encountered parsing data fields -167: [10:29:47] ERROR: moving to the beginning of the next molecule -167: [10:29:47] Spurious data before the first property will be ignored -167: [10:29:47] Property will be truncated after the first blank line -167: [10:29:47] Property will be truncated after the first blank line -167: [10:29:47] Property will be truncated after the first blank line -167: [10:29:47] ERROR: Problems encountered parsing data fields -167: [10:29:47] ERROR: moving to the beginning of the next molecule -167: [10:29:47] Property will be truncated after the first blank line -167: [10:29:47] ERROR: Problems encountered parsing data fields -167: [10:29:47] ERROR: moving to the beginning of the next molecule -167: [10:29:47] Property will be truncated after the first blank line -167: .[10:29:47] SMILES Parse Error: syntax error while parsing: fail -167: [10:29:47] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -167: [10:29:47] ERROR: Smiles parse error on line 2 -167: [10:29:47] ERROR: Cannot create molecule from : 'fail' +167: ..............[18:37:22] SMARTS Parse Error: syntax error while parsing: fiib +167: [18:37:22] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +167: ....[18:37:22] ERROR: Problems encountered parsing data fields +167: [18:37:22] ERROR: moving to the beginning of the next molecule +167: [18:37:22] ERROR: Problems encountered parsing data fields +167: [18:37:22] ERROR: moving to the beginning of the next molecule +167: [18:37:22] Spurious data before the first property will be ignored +167: [18:37:22] Property will be truncated after the first blank line +167: [18:37:22] Property will be truncated after the first blank line +167: [18:37:22] Property will be truncated after the first blank line +167: [18:37:22] ERROR: Problems encountered parsing data fields +167: [18:37:22] ERROR: moving to the beginning of the next molecule +167: [18:37:22] ERROR: Problems encountered parsing data fields +167: [18:37:22] ERROR: moving to the beginning of the next molecule +167: [18:37:22] Spurious data before the first property will be ignored +167: [18:37:22] Property will be truncated after the first blank line +167: [18:37:22] Property will be truncated after the first blank line +167: [18:37:22] Property will be truncated after the first blank line +167: [18:37:22] ERROR: Problems encountered parsing data fields +167: [18:37:22] ERROR: moving to the beginning of the next molecule +167: [18:37:22] Property will be truncated after the first blank line +167: [18:37:22] ERROR: Problems encountered parsing data fields +167: [18:37:22] ERROR: moving to the beginning of the next molecule +167: [18:37:22] Property will be truncated after the first blank line +167: .[18:37:22] SMILES Parse Error: syntax error while parsing: fail +167: [18:37:22] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +167: [18:37:22] ERROR: Smiles parse error on line 2 +167: [18:37:22] ERROR: Cannot create molecule from : 'fail' 167: >>> This may result in an infinite loop. It should finish almost instantly 167: <<< OK, it finished. -167: ............[10:29:47] Explicit valence for atom # 1 C, 5, is greater than permitted +167: ............[18:37:22] Explicit valence for atom # 1 C, 5, is greater than permitted 167: ........../build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rough_test.py:2161: DeprecationWarning: Please use assertEqual instead. 167: self.assertEquals(ri.NumRings(), 2) -167: ..[10:29:47] non-ring atom 0 marked aromatic -167: [10:29:47] non-ring atom 0 marked aromatic -167: [10:29:47] +167: ..[18:37:23] non-ring atom 0 marked aromatic +167: [18:37:23] non-ring atom 0 marked aromatic +167: [18:37:23] 167: 167: **** 167: Range Error @@ -38188,9 +38225,9 @@ 167: Failed Expression: 12 < 6 167: **** 167: -167: [10:29:47] non-ring atom 0 marked aromatic -167: [10:29:47] non-ring atom 0 marked aromatic -167: [10:29:47] +167: [18:37:23] non-ring atom 0 marked aromatic +167: [18:37:23] non-ring atom 0 marked aromatic +167: [18:37:23] 167: 167: **** 167: Range Error @@ -38199,35 +38236,40 @@ 167: Failed Expression: 12 < 6 167: **** 167: -167: ...............[10:29:47] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -167: [10:29:47] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. -167: ..............[10:29:47] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -167: [10:29:47] Explicit valence for atom # 1 C, 5, is greater than permitted -161: ............... -161: ---------------------------------------------------------------------- -161: Ran 15 tests in 6.012s -161: -161: OK -165/208 Test #161: pyRGroupDecomposition .................. Passed 6.93 sec +167: ...............[18:37:23] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +167: [18:37:23] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count. +167: ..............[18:37:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +167: [18:37:24] Explicit valence for atom # 1 C, 5, is greater than permitted +5: [18:37:40] Finished: testMultipleTimes() +5: [18:37:40] +5: ----------------------------------------- +164/208 Test #5: testConcurrentQueue .................... Passed 1163.55 sec test 168 Start 168: pyTestConformerWrap 168: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testConformer.py" 168: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 168: Test timeout computed to be: 1500 -168: ...... -168: ---------------------------------------------------------------------- -168: Ran 6 tests in 0.057s -168: -168: OK -166/208 Test #168: pyTestConformerWrap .................... Passed 0.87 sec +165/208 Test #158: testRGroupDecomp ....................... Passed 93.63 sec test 169 Start 169: pyTestTrajectory 169: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testTrajectory.py" 169: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 169: Test timeout computed to be: 1500 -169: [10:29:50] +168: ...... +168: ---------------------------------------------------------------------- +168: Ran 6 tests in 0.180s +168: +168: OK +166/208 Test #168: pyTestConformerWrap .................... Passed 3.23 sec +test 170 + Start 170: pyTestSGroups + +170: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testSGroups.py" +170: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap +170: Test timeout computed to be: 1500 +169: [18:37:44] 169: 169: **** 169: Pre-condition Violation @@ -38236,7 +38278,7 @@ 169: Failed Expression: from < static_cast(size()) 169: **** 169: -169: .[10:29:50] +169: .[18:37:44] 169: 169: **** 169: Pre-condition Violation @@ -38245,8 +38287,20 @@ 169: Failed Expression: from < static_cast(size()) 169: **** 169: -123: [10:29:51] done -169: .[10:29:51] +170: ............. +170: ---------------------------------------------------------------------- +170: Ran 13 tests in 0.315s +170: +170: OK +170: Testing SubstanceGroups wrapper +167/208 Test #170: pyTestSGroups .......................... Passed 3.51 sec +test 171 + Start 171: pyTestThreads + +171: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testThreads.py" +171: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap +171: Test timeout computed to be: 1500 +169: .[18:37:48] 169: 169: **** 169: Range Error @@ -38255,7 +38309,7 @@ 169: Failed Expression: 0 < 0 169: **** 169: -169: .[10:29:51] +169: .[18:37:48] 169: 169: **** 169: Pre-condition Violation @@ -38264,7 +38318,7 @@ 169: Failed Expression: traj.dimension() == 3 169: **** 169: -169: ..[10:29:51] +169: ..[18:37:48] 169: 169: **** 169: Pre-condition Violation @@ -38273,7 +38327,7 @@ 169: Failed Expression: traj.dimension() == 3 169: **** 169: -169: .[10:29:51] +169: .[18:37:48] 169: 169: **** 169: Pre-condition Violation @@ -38282,7 +38336,7 @@ 169: Failed Expression: d_pos 169: **** 169: -169: [10:29:51] +169: [18:37:48] 169: 169: **** 169: Pre-condition Violation @@ -38291,7 +38345,7 @@ 169: Failed Expression: d_trajectory 169: **** 169: -169: .[10:29:51] +169: .[18:37:48] 169: 169: **** 169: Range Error @@ -38300,7 +38354,7 @@ 169: Failed Expression: 5 < 5 169: **** 169: -169: [10:29:51] +169: [18:37:48] 169: 169: **** 169: Range Error @@ -38309,7 +38363,7 @@ 169: Failed Expression: 10 < 10 169: **** 169: -169: .[10:29:51] +169: .[18:37:48] 169: 169: **** 169: Range Error @@ -38318,7 +38372,7 @@ 169: Failed Expression: 5 < 5 169: **** 169: -169: [10:29:51] +169: [18:37:48] 169: 169: **** 169: Pre-condition Violation @@ -38327,7 +38381,7 @@ 169: Failed Expression: d_trajectory->dimension() == 2 169: **** 169: -169: [10:29:51] +169: [18:37:48] 169: 169: **** 169: Pre-condition Violation @@ -38338,172 +38392,128 @@ 169: 169: . 169: ---------------------------------------------------------------------- -169: Ran 9 tests in 1.292s +169: Ran 9 tests in 3.533s 169: 169: OK 169: Testing Trajectory wrapper -167/208 Test #169: pyTestTrajectory ....................... Passed 2.38 sec -test 170 - Start 170: pyTestSGroups - -170: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testSGroups.py" -170: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap -170: Test timeout computed to be: 1500 -170: ............. -170: ---------------------------------------------------------------------- -170: Ran 13 tests in 0.076s -170: -170: OK -170: Testing SubstanceGroups wrapper -168/208 Test #170: pyTestSGroups .......................... Passed 0.93 sec -test 171 - Start 171: pyTestThreads - -171: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testThreads.py" -171: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap -171: Test timeout computed to be: 1500 -171: [10:29:53] Warning: molecule is tagged as 3D, but all Z coords are zero -169/208 Test #171: pyTestThreads .......................... Passed 1.13 sec +168/208 Test #169: pyTestTrajectory ....................... Passed 6.72 sec test 172 Start 172: pyTestMultithreadedMolSupplier 172: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 172: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 172: Test timeout computed to be: 1500 +171: [18:37:50] Warning: molecule is tagged as 3D, but all Z coords are zero 172: .s. 172: ---------------------------------------------------------------------- -172: Ran 3 tests in 0.233s +172: Ran 3 tests in 0.610s 172: 172: OK (skipped=1) 172: Testing Smiles and SD MultithreadedMolSupplier -170/208 Test #172: pyTestMultithreadedMolSupplier ......... Passed 1.14 sec +169/208 Test #172: pyTestMultithreadedMolSupplier ......... Passed 3.46 sec test 173 Start 173: pyTestPropertyLists 173: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/testPropertyLists.py" 173: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 173: Test timeout computed to be: 1500 -173: [10:29:55] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [10:29:55] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [10:29:55] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -173: .[10:29:55] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [10:29:55] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [10:29:55] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -173: ..[10:29:55] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [10:29:55] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [10:29:55] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: [18:37:54] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [18:37:54] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [18:37:54] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: .[18:37:54] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [18:37:54] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [18:37:54] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: ..[18:37:54] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [18:37:54] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [18:37:54] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 173: . 173: ---------------------------------------------------------------------- -173: Ran 4 tests in 0.034s +173: Ran 4 tests in 0.102s 173: 173: OK -171/208 Test #173: pyTestPropertyLists .................... Passed 0.83 sec +170/208 Test #173: pyTestPropertyLists .................... Passed 2.73 sec test 174 Start 174: pyCDXMLTest 174: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/test_cdxml.py" 174: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 174: Test timeout computed to be: 1500 -174: . -174: ---------------------------------------------------------------------- -174: Ran 1 test in 0.056s -174: -174: OK -172/208 Test #174: pyCDXMLTest ............................ Passed 1.01 sec +171/208 Test #171: pyTestThreads .......................... Passed 8.89 sec test 175 Start 175: molStandardizeTest 175: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molStandardizeTest 175: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 175: Test timeout computed to be: 1500 -173/208 Test #175: molStandardizeTest ..................... Passed 3.55 sec +174: . +174: ---------------------------------------------------------------------- +174: Ran 1 test in 0.109s +174: +174: OK +172/208 Test #174: pyCDXMLTest ............................ Passed 3.00 sec test 176 Start 176: molNormalizeTest 176: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molNormalizeTest 176: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 176: Test timeout computed to be: 1500 -176: [10:30:00] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -176: [10:30:00] Initializing Normalizer -176: [10:30:00] Running Normalizer -176: [10:30:01] Rule applied: BrokenazidetoN=N+=N- -176: [10:30:01] Initializing Normalizer -176: [10:30:01] Running Normalizer -176: [10:30:01] Initializing Normalizer -176: [10:30:01] Running Normalizer -174/208 Test #176: molNormalizeTest ....................... Passed 0.48 sec +167: ...........................[18:37:58] unable to set wavy bonds for double bonds: 3 +176: [18:37:58] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +167: .........[18:37:58] +167: +167: **** +167: Range Error +167: idx +167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +167: Failed Expression: 6 < 5 +167: **** +167: +176: [18:37:59] Initializing Normalizer +176: [18:37:59] Running Normalizer +176: [18:37:59] Rule applied: BrokenazidetoN=N+=N- +176: [18:37:59] Initializing Normalizer +176: [18:37:59] Running Normalizer +176: [18:37:59] Initializing Normalizer +176: [18:37:59] Running Normalizer +173/208 Test #176: molNormalizeTest ....................... Passed 1.27 sec test 177 Start 177: molValidateTest 177: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molValidateTest 177: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 177: Test timeout computed to be: 1500 -175/208 Test #177: molValidateTest ........................ Passed 0.19 sec +174/208 Test #177: molValidateTest ........................ Passed 0.51 sec test 178 Start 178: molChargeTest 178: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molChargeTest 178: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 178: Test timeout computed to be: 1500 -167: ...........................[10:30:01] unable to set wavy bonds for double bonds: 3 -176/208 Test #178: molChargeTest .......................... Passed 0.35 sec +175/208 Test #178: molChargeTest .......................... Passed 1.16 sec test 179 Start 179: molTautomerTest 179: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molTautomerTest 179: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 179: Test timeout computed to be: 1500 -167: .........[10:30:01] -167: -167: **** -167: Range Error -167: idx -167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -167: Failed Expression: 6 < 5 -167: **** -167: -179: [10:30:03] Tautomer enumeration stopped at 292 tautomers: max transforms reached -179: [10:30:07] Tautomer enumeration stopped at 292 tautomers: max transforms reached -179: [10:30:07] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -179: [10:30:08] Tautomer enumeration stopped at 14 tautomers: canceled -179: Enumeration was canceled due to timeout (50 ms) -167: ...................[10:30:09] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:09] Explicit valence for atom # 6 F, 2, is greater than permitted -167: [10:30:09] Can't kekulize mol. Unkekulized atoms: 3 4 5 -167: .[10:30:09] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [10:30:09] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [10:30:09] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [10:30:09] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [10:30:09] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [10:30:09] Warning: molecule is tagged as 3D, but all Z coords are zero -179: 375 -179: Enumeration has completed -179: [10:30:10] Tautomer enumeration stopped at 22 tautomers: canceled -123: CNC[C@H]1CC[C@H](C[NH3+])CC1 -179: CN=c1cc[nH]cn1 -179: CN=c1ccnc[nH]1 -179: CNc1ccncn1 -179: res: CNc1ccncn1 -179: CN=c1cccc[nH]1 -179: CNc1ccccn1 -179: res: CNc1ccccn1 -177/208 Test #179: molTautomerTest ........................ Passed 12.11 sec +176/208 Test #175: molStandardizeTest ..................... Passed 11.02 sec test 180 Start 180: molStandardizeSmallTest 180: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molStandardizeSmallTest 180: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 180: Test timeout computed to be: 1500 -178/208 Test #180: molStandardizeSmallTest ................ Passed 0.18 sec +177/208 Test #180: molStandardizeSmallTest ................ Passed 0.51 sec test 181 Start 181: molFragmentTest 181: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molFragmentTest 181: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 181: Test timeout computed to be: 1500 -181: [10:30:14] SMARTS Parse Error: syntax error while parsing: [Cl -181: [10:30:14] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -179/208 Test #181: molFragmentTest ........................ Passed 0.18 sec +179: [18:38:08] Tautomer enumeration stopped at 292 tautomers: max transforms reached +181: [18:38:08] SMARTS Parse Error: syntax error while parsing: [Cl +181: [18:38:08] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +178/208 Test #181: molFragmentTest ........................ Passed 0.67 sec test 182 Start 182: molStandardizeCatchTest @@ -38514,247 +38524,123 @@ 182: * - * - * - * m2 182: * - * - * - * m1 182: * - * - * - * m2 -182: [10:30:14] Can't kekulize mol. Unkekulized atoms: 3 7 -182: [10:30:15] Can't kekulize mol. Unkekulized atoms: 3 8 -182: [10:30:15] Can't kekulize mol. Unkekulized atoms: 2 3 4 +182: [18:38:11] Can't kekulize mol. Unkekulized atoms: 3 7 +182: [18:38:11] Can't kekulize mol. Unkekulized atoms: 3 8 +182: [18:38:11] Can't kekulize mol. Unkekulized atoms: 2 3 4 182: =============================================================================== 182: All tests passed (240 assertions in 36 test cases) 182: -180/208 Test #182: molStandardizeCatchTest ................ Passed 0.96 sec +179/208 Test #182: molStandardizeCatchTest ................ Passed 2.99 sec test 183 Start 183: pyMolStandardize 183: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 183: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap 183: Test timeout computed to be: 1500 -123: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 -183: .....[10:30:17] Tautomer enumeration stopped at 292 tautomers: max transforms reached -123: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 -183: [10:30:17] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -123: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 -183: .[10:30:18] Tautomer enumeration stopped at 21 tautomers: canceled +179: [18:38:13] Tautomer enumeration stopped at 292 tautomers: max transforms reached +167: ...................[18:38:13] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:13] Explicit valence for atom # 6 F, 2, is greater than permitted +167: [18:38:13] Can't kekulize mol. Unkekulized atoms: 3 4 5 +167: .[18:38:13] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [18:38:13] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [18:38:13] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [18:38:13] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [18:38:13] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [18:38:13] Warning: molecule is tagged as 3D, but all Z coords are zero +179: [18:38:13] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +179: [18:38:15] Tautomer enumeration stopped at 11 tautomers: canceled +179: Enumeration was canceled due to timeout (50 ms) +183: .....[18:38:20] Tautomer enumeration stopped at 292 tautomers: max transforms reached +183: [18:38:21] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +179: 375 +179: Enumeration has completed +179: [18:38:22] Tautomer enumeration stopped at 11 tautomers: canceled +183: .[18:38:23] Tautomer enumeration stopped at 11 tautomers: canceled 183: Enumeration was canceled due to timeout (50 ms) -123: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 -183: Enumeration has completed -183: [10:30:22] Tautomer enumeration stopped at 21 tautomers: canceled -167: ...............[10:30:24] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: [10:30:24] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: [10:30:24] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: [10:30:24] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: [10:30:24] -167: -167: **** -167: Pre-condition Violation -167: no owner -167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -167: Failed Expression: dp_mol -167: **** -167: -167: .....[10:30:24] -167: -167: **** -167: Range Error -167: atomIdx1 -167: Violation occurred on line 331 in file ./Code/GraphMol/RWMol.cpp -167: Failed Expression: 0 < 0 -167: **** -167: -167: ......[10:30:24] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -167: [10:30:24] ERROR: Smiles parse error on line 0 -167: [10:30:24] ERROR: Cannot create molecule from : 'c1ccccc' -167: [10:30:24] SMILES Parse Error: extra open parentheses for input: 'C(C' -167: [10:30:24] ERROR: Smiles parse error on line 3 -167: [10:30:24] ERROR: Cannot create molecule from : 'C(C' -167: [10:30:24] Explicit valence for atom # 1 C, 5, is greater than permitted -167: [10:30:24] ERROR: Could not sanitize molecule on line 6 -167: [10:30:24] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -167: [10:30:24] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -167: [10:30:24] ERROR: Smiles parse error on line 0 -167: [10:30:24] ERROR: Cannot create molecule from : 'c1ccccc' -167: [10:30:24] SMILES Parse Error: extra open parentheses for input: 'C(C' -167: [10:30:24] ERROR: Smiles parse error on line 3 -167: [10:30:24] ERROR: Cannot create molecule from : 'C(C' -167: [10:30:24] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -167: [10:30:24] ERROR: Smiles parse error on line 6 -167: [10:30:24] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -167: [10:30:24] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:24] ERROR: Could not sanitize molecule ending on line 21 -167: [10:30:24] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:24] ERROR: EOF hit while reading atoms -167: [10:30:24] ERROR: moving to the beginning of the next molecule -167: [10:30:24] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:24] ERROR: Could not sanitize molecule ending on line 21 -167: [10:30:24] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:24] ERROR: EOF hit while reading atoms -167: [10:30:24] ERROR: moving to the beginning of the next molecule -167: ....[10:30:24] -167: -167: **** -167: Pre-condition Violation -167: RingInfo not initialized -167: Violation occurred on line 169 in file ./Code/GraphMol/RingInfo.cpp -167: Failed Expression: df_init -167: **** -167: -123: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O -167: ......[10:30:24] -167: -167: **** -167: Range Error -167: idx -167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -167: Failed Expression: 3 < 1 -167: **** -167: -183: ...............[10:30:24] Explicit valence for atom # 1 O, 3, is greater than permitted -167: ..[10:30:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -183: . -183: ---------------------------------------------------------------------- -183: Ran 22 tests in 8.270s -183: -183: OK -183: done -181/208 Test #183: pyMolStandardize ....................... Passed 9.44 sec +123: [18:38:27] done +179: CN=c1cc[nH]cn1 +179: CN=c1ccnc[nH]1 +179: CNc1ccncn1 +179: res: CNc1ccncn1 +179: CN=c1cccc[nH]1 +179: CNc1ccccn1 +179: res: CNc1ccccn1 +180/208 Test #179: molTautomerTest ........................ Passed 29.24 sec test 184 Start 184: testScaffoldNetwork 184: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 184: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork 184: Test timeout computed to be: 1500 -167: .................[10:30:24] SMILES Parse Error: unclosed ring for input: 'C1CC' -167: ......[10:30:24] WARNING: not removing hydrogen atom without neighbors -167: [10:30:24] WARNING: not removing hydrogen atom with dummy atom neighbors -167: [10:30:24] WARNING: not removing hydrogen atom with wedged bond -167: [10:30:24] WARNING: not removing hydrogen atom without neighbors -167: [10:30:24] WARNING: not removing hydrogen atom with dummy atom neighbors -123: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O -167: .....[10:30:25] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: .[10:30:25] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:25] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:25] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:25] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [10:30:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: [10:30:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: [10:30:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: ..........[10:30:25] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -167: [10:30:25] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -167: .[10:30:25] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -167: [10:30:25] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -167: ..[10:30:25] SMILES Parse Error: syntax error while parsing: error -167: [10:30:25] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -167: [10:30:25] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -167: [10:30:25] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -167: [10:30:25] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -167: ...........[10:30:25] SMILES Parse Error: syntax error while parsing: garbage_0 -167: [10:30:25] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -167: [10:30:25] SMILES Parse Error: syntax error while parsing: garbage_2 -167: [10:30:25] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -167: [10:30:25] SMILES Parse Error: syntax error while parsing: garbage_4 -167: [10:30:25] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -167: ......... -167: ---------------------------------------------------------------------- -167: Ran 228 tests in 38.761s -167: -167: OK -167: 1 -167: supplier: -167: supplier: -167: supplier: -182/208 Test #167: pyGraphMolWrap ......................... Passed 40.33 sec +183: [18:38:33] Tautomer enumeration stopped at 362 tautomers: canceled +183: Enumeration was canceled due to timeout (10 s) +183: [18:38:33] Tautomer enumeration stopped at 5 tautomers: canceled +183: ...............[18:38:37] Explicit valence for atom # 1 O, 3, is greater than permitted +183: . +183: ---------------------------------------------------------------------- +183: Ran 22 tests in 22.994s +183: +183: OK +183: done +181/208 Test #183: pyMolStandardize ....................... Passed 26.81 sec test 185 Start 185: pyScaffoldNetwork 185: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 185: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap 185: Test timeout computed to be: 1500 -123: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O -123: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O -185: ....... -185: ---------------------------------------------------------------------- -185: Ran 7 tests in 0.151s -185: -185: OK -183/208 Test #185: pyScaffoldNetwork ...................... Passed 1.09 sec +184: =============================================================================== +184: All tests passed (266 assertions in 18 test cases) +184: +182/208 Test #184: testScaffoldNetwork .................... Passed 10.38 sec test 186 Start 186: pyScaffoldNetworkPickling 186: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 186: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap 186: Test timeout computed to be: 1500 -123: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC -186: . -186: ---------------------------------------------------------------------- -186: Ran 1 test in 0.046s -186: -186: OK -184/208 Test #186: pyScaffoldNetworkPickling .............. Passed 0.90 sec +185: ....... +185: ---------------------------------------------------------------------- +185: Ran 7 tests in 0.445s +185: +185: OK +183/208 Test #185: pyScaffoldNetwork ...................... Passed 3.40 sec test 187 Start 187: testMolEnumerator 187: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/testMolEnumerator 187: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator 187: Test timeout computed to be: 1500 -184: =============================================================================== -184: All tests passed (266 assertions in 18 test cases) -184: -185/208 Test #184: testScaffoldNetwork .................... Passed 3.77 sec +187: [18:38:42] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +187: =============================================================================== +187: All tests passed (247 assertions in 12 test cases) +187: +184/208 Test #187: testMolEnumerator ...................... Passed 0.69 sec test 188 Start 188: pyMolEnumerator 188: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 188: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap 188: Test timeout computed to be: 1500 -187: [10:30:28] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -187: =============================================================================== -187: All tests passed (247 assertions in 12 test cases) -187: -186/208 Test #187: testMolEnumerator ...................... Passed 0.25 sec +186: . +186: ---------------------------------------------------------------------- +186: Ran 1 test in 0.113s +186: +186: OK +185/208 Test #186: pyScaffoldNetworkPickling .............. Passed 2.86 sec test 189 Start 189: testAbbreviations 189: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/testAbbreviations 189: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations 189: Test timeout computed to be: 1500 -189: [10:30:28] SMARTS Parse Error: syntax error while parsing: *fail -189: [10:30:28] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -189: [10:30:28] no suitable SubstanceGroups found +189: [18:38:43] SMARTS Parse Error: syntax error while parsing: *fail +189: [18:38:43] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +189: [18:38:43] no suitable SubstanceGroups found 189: =============================================================================== 189: All tests passed (195 assertions in 12 test cases) 189: -187/208 Test #189: testAbbreviations ...................... Passed 0.16 sec +186/208 Test #189: testAbbreviations ...................... Passed 0.39 sec test 190 Start 190: pyAbbreviations @@ -38763,10 +38649,10 @@ 190: Test timeout computed to be: 1500 188: ... 188: ---------------------------------------------------------------------- -188: Ran 3 tests in 0.043s +188: Ran 3 tests in 0.120s 188: 188: OK -188/208 Test #188: pyMolEnumerator ........................ Passed 0.88 sec +187/208 Test #188: pyMolEnumerator ........................ Passed 2.78 sec test 191 Start 191: testQuery @@ -38790,7 +38676,7 @@ 191: XOr 191: pointer and copy foo 191: Set2 -189/208 Test #191: testQuery .............................. Passed 0.02 sec +188/208 Test #191: testQuery .............................. Passed 0.07 sec test 192 Start 192: testMatCalc @@ -38842,7 +38728,7 @@ 192: 9.49496e+07 192: 2.25618e+08 192: 1.30219e+08 -190/208 Test #192: testMatCalc ............................ Passed 0.02 sec +189/208 Test #192: testMatCalc ............................ Passed 0.04 sec test 193 Start 193: pyMatCalc @@ -38851,23 +38737,23 @@ 193: Test timeout computed to be: 1500 190: ....... 190: ---------------------------------------------------------------------- -190: Ran 7 tests in 0.071s +190: Ran 7 tests in 0.193s 190: 190: OK -191/208 Test #190: pyAbbreviations ........................ Passed 0.94 sec +190/208 Test #190: pyAbbreviations ........................ Passed 2.81 sec test 194 Start 194: testSimDivPickers 194: Test command: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/testSimDivPickers 194: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers 194: Test timeout computed to be: 1500 -194: [10:30:30] ------------------------------------- -194: [10:30:30] Testing github issue 1421: MaxMinPicker picking non-existent element. -194: [10:30:30] Done -194: [10:30:30] ------------------------------------- -194: [10:30:30] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -194: [10:30:30] Done -192/208 Test #194: testSimDivPickers ...................... Passed 1.14 sec +194: [18:38:46] ------------------------------------- +194: [18:38:46] Testing github issue 1421: MaxMinPicker picking non-existent element. +194: [18:38:46] Done +194: [18:38:46] ------------------------------------- +194: [18:38:46] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +194: [18:38:46] Done +191/208 Test #194: testSimDivPickers ...................... Passed 0.05 sec test 195 Start 195: pickersTestsCatch @@ -38877,33 +38763,139 @@ 195: =============================================================================== 195: All tests passed (21267 assertions in 1 test case) 195: -193/208 Test #195: pickersTestsCatch ...................... Passed 0.39 sec +192/208 Test #195: pickersTestsCatch ...................... Passed 0.75 sec test 196 Start 196: pySimDivPickers 196: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/testPickers.py" 196: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap 196: Test timeout computed to be: 1500 -196: [10:30:31] the useCache argument is deprecated and ignored +196: [18:38:49] the useCache argument is deprecated and ignored +167: ...............[18:38:51] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: [18:38:51] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: [18:38:51] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: [18:38:51] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: [18:38:51] +167: +167: **** +167: Pre-condition Violation +167: no owner +167: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +167: Failed Expression: dp_mol +167: **** +167: +167: .....[18:38:51] +167: +167: **** +167: Range Error +167: atomIdx1 +167: Violation occurred on line 331 in file ./Code/GraphMol/RWMol.cpp +167: Failed Expression: 0 < 0 +167: **** +167: +167: ......[18:38:51] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +167: [18:38:51] ERROR: Smiles parse error on line 0 +167: [18:38:51] ERROR: Cannot create molecule from : 'c1ccccc' +167: [18:38:51] SMILES Parse Error: extra open parentheses for input: 'C(C' +167: [18:38:51] ERROR: Smiles parse error on line 3 +167: [18:38:51] ERROR: Cannot create molecule from : 'C(C' +167: [18:38:51] Explicit valence for atom # 1 C, 5, is greater than permitted +167: [18:38:51] ERROR: Could not sanitize molecule on line 6 +167: [18:38:51] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +167: [18:38:51] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +167: [18:38:51] ERROR: Smiles parse error on line 0 +167: [18:38:51] ERROR: Cannot create molecule from : 'c1ccccc' +167: [18:38:51] SMILES Parse Error: extra open parentheses for input: 'C(C' +167: [18:38:51] ERROR: Smiles parse error on line 3 +167: [18:38:51] ERROR: Cannot create molecule from : 'C(C' +167: [18:38:51] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +167: [18:38:51] ERROR: Smiles parse error on line 6 +167: [18:38:51] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +167: [18:38:51] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:51] ERROR: Could not sanitize molecule ending on line 21 +167: [18:38:51] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:51] ERROR: EOF hit while reading atoms +167: [18:38:51] ERROR: moving to the beginning of the next molecule +167: [18:38:51] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:51] ERROR: Could not sanitize molecule ending on line 21 +167: [18:38:51] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:51] ERROR: EOF hit while reading atoms +167: [18:38:51] ERROR: moving to the beginning of the next molecule +196: ...[18:38:51] the useCache argument is deprecated and ignored +196: [18:38:51] the useCache argument is deprecated and ignored 193: ..... 193: ---------------------------------------------------------------------- -193: Ran 5 tests in 1.300s +193: Ran 5 tests in 4.180s 193: 193: OK -194/208 Test #193: pyMatCalc .............................. Passed 2.95 sec +167: ....[18:38:51] +167: +167: **** +167: Pre-condition Violation +167: RingInfo not initialized +167: Violation occurred on line 169 in file ./Code/GraphMol/RingInfo.cpp +167: Failed Expression: df_init +167: **** +167: +196: .[18:38:51] the useCache argument is deprecated and ignored +167: ......[18:38:51] +167: +167: **** +167: Range Error +167: idx +167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +167: Failed Expression: 3 < 1 +167: **** +167: +167: ..[18:38:51] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +193/208 Test #193: pyMatCalc .............................. Passed 6.42 sec test 197 Start 197: pyRanker 197: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/testRanker.py" 197: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap 197: Test timeout computed to be: 1500 -196: ...[10:30:32] the useCache argument is deprecated and ignored -196: [10:30:32] the useCache argument is deprecated and ignored -196: .[10:30:32] the useCache argument is deprecated and ignored -123: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O +167: .................[18:38:52] SMILES Parse Error: unclosed ring for input: 'C1CC' +167: ......[18:38:52] WARNING: not removing hydrogen atom without neighbors +167: [18:38:52] WARNING: not removing hydrogen atom with dummy atom neighbors +167: [18:38:52] WARNING: not removing hydrogen atom with wedged bond +167: [18:38:52] WARNING: not removing hydrogen atom without neighbors +167: [18:38:52] WARNING: not removing hydrogen atom with dummy atom neighbors 197: ../build/reproducible-path/rdkit-202209.3/Code/ML/InfoTheory/Wrap/testRanker.py:124: DeprecationWarning: Please use assertRaisesRegex instead. 197: with self.assertRaisesRegexp(Exception, ""): -197: [10:30:32] +197: [18:38:54] 197: 197: **** 197: Invariant Violation @@ -38914,10 +38906,10 @@ 197: 197: ... 197: ---------------------------------------------------------------------- -197: Ran 5 tests in 0.129s +197: Ran 5 tests in 0.222s 197: 197: OK -195/208 Test #197: pyRanker ............................... Passed 1.03 sec +194/208 Test #197: pyRanker ............................... Passed 2.65 sec test 198 Start 198: testChemicalFeatures @@ -38927,61 +38919,86 @@ 198: ----------------------------------------- 198: Test1 198: Done -196/208 Test #198: testChemicalFeatures ................... Passed 0.09 sec +195/208 Test #198: testChemicalFeatures ................... Passed 0.05 sec test 199 Start 199: pyFeatures 199: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/testFeatures.py" 199: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap 199: Test timeout computed to be: 1500 +167: .....[18:38:55] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: .[18:38:55] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:55] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:55] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:55] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [18:38:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: [18:38:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: [18:38:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: ..........[18:38:55] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +167: [18:38:55] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +167: .[18:38:55] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +167: [18:38:55] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +167: ..[18:38:55] SMILES Parse Error: syntax error while parsing: error +167: [18:38:55] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +167: [18:38:55] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +167: [18:38:55] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +167: [18:38:55] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +167: ...........[18:38:56] SMILES Parse Error: syntax error while parsing: garbage_0 +167: [18:38:56] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +167: [18:38:56] SMILES Parse Error: syntax error while parsing: garbage_2 +167: [18:38:56] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +167: [18:38:56] SMILES Parse Error: syntax error while parsing: garbage_4 +167: [18:38:56] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +167: ......... +167: ---------------------------------------------------------------------- +167: Ran 228 tests in 94.587s +167: +167: OK +167: 1 +167: supplier: +167: supplier: +167: supplier: 199: .. 199: ---------------------------------------------------------------------- -199: Ran 2 tests in 0.053s +199: Ran 2 tests in 0.016s 199: 199: OK 199: Testing ChemicalFeatures Wrapper code: -197/208 Test #199: pyFeatures ............................. Passed 0.91 sec +196/208 Test #167: pyGraphMolWrap ......................... Passed 99.34 sec test 200 Start 200: pythonTestDbCLI 200: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/Projects" 200: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/Projects 200: Test timeout computed to be: 1500 -196: ....... -196: ---------------------------------------------------------------------- -196: Ran 11 tests in 4.965s -196: -196: OK -198/208 Test #196: pySimDivPickers ........................ Passed 5.65 sec +197/208 Test #199: pyFeatures ............................. Passed 2.52 sec test 201 Start 201: pythonTestDirRoot 201: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit" 201: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit 201: Test timeout computed to be: 1500 -200: [10:30:37] INFO: Reading molecules and constructing molecular database. -200: -200: [10:30:37] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [10:30:37] INFO: Processing 10 molecules -200: -200: [10:30:37] INFO: Generating fingerprints and descriptors: -200: 201: ......................... 201: ---------------------------------------------------------------------- -201: Ran 25 tests in 0.630s +201: Ran 25 tests in 1.965s 201: 201: OK -200: [10:30:37] INFO: Finished. -200: -199/208 Test #201: pythonTestDirRoot ...................... Passed 1.23 sec +198/208 Test #201: pythonTestDirRoot ...................... Passed 3.70 sec test 202 Start 202: pythonTestDirML 202: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/ML/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/ML" 202: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit 202: Test timeout computed to be: 1500 -123: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 +200: [18:39:04] INFO: Reading molecules and constructing molecular database. +200: +200: [18:39:04] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [18:39:04] INFO: Processing 10 molecules +200: +200: [18:39:05] INFO: Generating fingerprints and descriptors: +200: 202: EEEEEEE 202: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -39103,15 +39120,23 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 7 tests in 0.235s +202: Ran 7 tests in 0.771s 202: 202: FAILED (errors=7) -200: [10:30:40] INFO: Reading molecules and constructing molecular database. -200: -200: [10:30:40] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [10:30:40] INFO: Processing 163 molecules +196: ....... +196: ---------------------------------------------------------------------- +196: Ran 11 tests in 16.491s +196: +196: OK +200: [18:39:06] INFO: Finished. 200: +199/208 Test #196: pySimDivPickers ........................ Passed 18.86 sec +test 203 + Start 203: pythonTestDirDataStructs + +203: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/DataStructs" +203: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit +203: Test timeout computed to be: 1500 202: EEEEEEEEEEEE 202: ====================================================================== 202: ERROR: test10_filtering (__main__.TestCase.test10_filtering) @@ -39318,12 +39343,16 @@ 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ---------------------------------------------------------------------- -202: Ran 12 tests in 0.171s +202: Ran 12 tests in 0.726s 202: 202: FAILED (errors=12) -123: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 -200: [10:30:40] INFO: done 100 -200: +203: ....... +203: ---------------------------------------------------------------------- +203: Ran 7 tests in 0.204s +203: +203: OK +203: ............../build/reproducible-path/rdkit-202209.3/rdkit/DataStructs/UnitTestcBitVect.py:42: DeprecationWarning: Please use assertRaisesRegex instead. +203: with self.assertRaisesRegexp(IndexError, ""): 202: Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/UnitTestAnalyzeComposite.py", line 44, in test1_Issue163 202: res = sorted(AnalyzeComposite.ProcessIt([c1, c2], verbose=-1)) @@ -39337,6 +39366,11 @@ 202: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. 202: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +203: .................... +203: ---------------------------------------------------------------------- +203: Ran 34 tests in 0.048s +203: +203: OK 202: F 202: ====================================================================== 202: FAIL: test1_Issue163 (__main__.TestCase.test1_Issue163) @@ -39347,28 +39381,86 @@ 202: AssertionError: 0 is not true 202: 202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.093s +202: Ran 1 test in 0.363s 202: 202: FAILED (failures=1) -200: [10:30:41] INFO: Generating fingerprints and descriptors: +200: [18:39:13] INFO: Reading molecules and constructing molecular database. 200: -123: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 +200: [18:39:13] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [18:39:13] INFO: Processing 163 molecules +200: +200: [18:39:14] INFO: done 100 +200: +203: ..... +203: ---------------------------------------------------------------------- +203: Ran 5 tests in 0.218s +203: +203: OK 202: ... 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.005s +202: Ran 3 tests in 0.016s 202: 202: OK +200: [18:39:16] INFO: Generating fingerprints and descriptors: +200: +203: ....... +203: ---------------------------------------------------------------------- +203: Ran 7 tests in 0.016s +203: +203: OK +200/208 Test #203: pythonTestDirDataStructs ............... Passed 11.58 sec +test 204 + Start 204: pythonTestDirDbase + +204: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/Dbase" +204: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit +204: Test timeout computed to be: 1500 +123: CNC[C@H]1CC[C@H](C[NH3+])CC1 202: ........ 202: ---------------------------------------------------------------------- -202: Ran 8 tests in 0.002s +202: Ran 8 tests in 0.014s 202: 202: OK -123: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 +204: .. +204: ---------------------------------------------------------------------- +204: Ran 2 tests in 0.277s +204: +204: OK +204: ........... +204: ---------------------------------------------------------------------- +204: Ran 11 tests in 0.452s +204: +204: OK +204: . +204: ---------------------------------------------------------------------- +204: Ran 1 test in 0.015s +204: +204: OK 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.603s +202: Ran 4 tests in 1.488s 202: 202: OK +204: ../build/reproducible-path/rdkit-202209.3/rdkit/Dbase/UnitTestDbUtils.py:96: DeprecationWarning: Please use assertRaisesRegex instead. +204: with self.assertRaisesRegexp(IndexError, ""): +204: ............. +204: ---------------------------------------------------------------------- +204: Ran 15 tests in 0.236s +204: +204: OK +204: ...... +204: ---------------------------------------------------------------------- +204: Ran 6 tests in 0.062s +204: +204: OK +201/208 Test #204: pythonTestDirDbase ..................... Passed 6.21 sec +test 205 + Start 205: pythonTestDirSimDivFilters + +205: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/SimDivFilters" +205: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit +205: Test timeout computed to be: 1500 202: E.EEE 202: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -39427,9 +39519,16 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.013s +202: Ran 5 tests in 0.037s 202: 202: FAILED (errors=4) +202/208 Test #205: pythonTestDirSimDivFilters ............. Passed 3.44 sec +test 206 + Start 206: pythonTestDirVLib + +206: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/VLib" +206: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit +206: Test timeout computed to be: 1500 202: .......E. 202: ====================================================================== 202: ERROR: test_RandomizeActivities (__main__.TestCase.test_RandomizeActivities) @@ -39442,21 +39541,37 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 9 tests in 0.031s +202: Ran 9 tests in 0.052s 202: 202: FAILED (errors=1) +206: ............. +206: ---------------------------------------------------------------------- +206: Ran 13 tests in 0.110s +206: +206: OK 202: ............ 202: ---------------------------------------------------------------------- -202: Ran 12 tests in 0.017s +202: Ran 12 tests in 0.027s 202: 202: OK -123: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.111s +202: Ran 5 tests in 0.197s 202: 202: OK -123: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O +206: ........... +206: ---------------------------------------------------------------------- +206: Ran 11 tests in 0.464s +206: +206: OK +203/208 Test #206: pythonTestDirVLib ...................... Passed 5.68 sec +test 207 + Start 207: pythonTestSping + +207: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/sping" +207: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit +207: Test timeout computed to be: 1500 +123: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 208, in __main__.SplitDbData 202: Failed example: @@ -39650,37 +39765,80 @@ 202: 8 of 16 in __main__.SplitDbData 202: 6 of 22 in __main__.SplitIndices 202: ***Test Failed*** 14 failures. +123: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 +123: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 202: !!! TEST FAILURE: python UnitTestFilter.py {} 202: !!! TEST FAILURE: python UnitTestMLData.py {} 202: !!! TEST FAILURE: python SplitData.py {} +207: .. +207: ---------------------------------------------------------------------- +207: Ran 2 tests in 2.070s +207: +207: OK 202: . 202: ---------------------------------------------------------------------- 202: Ran 1 test in 0.001s 202: 202: OK +204/208 Test #207: pythonTestSping ........................ Passed 6.77 sec +test 208 + Start 208: pythonTestDirChem + +208: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/Chem" "--buildType" "None" +208: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem +208: Test timeout computed to be: 1500 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.007s +202: Ran 6 tests in 0.012s 202: 202: OK -123: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 1.149s +202: Ran 4 tests in 1.819s 202: 202: OK +208: ....... +208: ---------------------------------------------------------------------- +208: Ran 7 tests in 0.956s +208: +208: OK +123: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.132s +202: Ran 6 tests in 0.180s 202: 202: OK -200: [10:30:58] INFO: Finished. +208: ...... +208: ---------------------------------------------------------------------- +208: Ran 6 tests in 0.166s +208: +208: OK +200: [18:39:47] INFO: Finished. 200: +208: ....[18:39:49] +208: +208: **** +208: Pre-condition Violation +208: valence not defined for atoms not associated with molecules +208: Violation occurred on line 422 in file ./Code/GraphMol/Atom.cpp +208: Failed Expression: dp_mol +208: **** +208: +208: . +208: ---------------------------------------------------------------------- +208: Ran 5 tests in 0.085s +208: +208: OK 202: .. 202: ---------------------------------------------------------------------- -202: Ran 2 tests in 0.648s +202: Ran 2 tests in 1.214s 202: 202: OK +208: .... +208: ---------------------------------------------------------------------- +208: Ran 4 tests in 0.088s +208: +208: OK 202: ........E. 202: ====================================================================== 202: ERROR: test8RandomForest (__main__.TestCase.test8RandomForest) @@ -39697,21 +39855,33 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 10 tests in 0.035s +202: Ran 10 tests in 0.123s 202: 202: FAILED (errors=1) -123: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +208: .. +208: ---------------------------------------------------------------------- +208: Ran 2 tests in 0.089s +208: +208: OK +123: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.529s +202: Ran 5 tests in 0.714s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestQuantTree.py {} +208: ...................... +208: ---------------------------------------------------------------------- +208: Ran 22 tests in 0.334s +208: +208: OK +123: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 202: .. 202: ---------------------------------------------------------------------- -202: Ran 2 tests in 0.013s +202: Ran 2 tests in 0.033s 202: 202: OK +123: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 202: ....Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/ML/Descriptors/MoleculeDescriptors.py", line 88, in CalcDescriptors 202: res[i] = fn(mol) @@ -39738,16 +39908,42 @@ 202: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 202: 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.087s +202: Ran 5 tests in 0.132s 202: 202: FAILED (errors=1) -123: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +123: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O +208: .....s..........E......ss +208: ====================================================================== +208: ERROR: testIpc (__main__.TestCase.testIpc) +208: ---------------------------------------------------------------------- +208: Traceback (most recent call last): +208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestGraphDescriptors_2.py", line 112, in testIpc +208: Ipc = GraphDescriptors.Ipc(m, forceDMat=1) +208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +208: File "/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc +208: cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) +208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +208: File "/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial +208: res = numpy.zeros(nAtoms + 1, numpy.float) +208: ^^^^^^^^^^^ +208: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ +208: raise AttributeError(__former_attrs__[attr]) +208: AttributeError: module 'numpy' has no attribute 'float'. +208: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. +208: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: +208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +208: +208: ---------------------------------------------------------------------- +208: Ran 25 tests in 1.277s +208: +208: FAILED (errors=1, skipped=3) 202: ... 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.063s +202: Ran 3 tests in 0.102s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestMolDescriptors.py {} +123: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 202: EEE 202: ====================================================================== 202: ERROR: test0CorrMat (__main__.TestCase.test0CorrMat) @@ -39774,16 +39970,40 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.014s +202: Ran 3 tests in 0.020s 202: 202: FAILED (errors=3) 202: !!! TEST FAILURE: python UnitTestCorrMatGen.py {} +208: ..s +208: ---------------------------------------------------------------------- +208: Ran 3 tests in 1.464s +208: +208: OK (skipped=1) +208: ................................... +208: ---------------------------------------------------------------------- +208: Ran 35 tests in 1.257s +208: +208: OK +208: .... +208: ---------------------------------------------------------------------- +208: Ran 4 tests in 0.166s +208: +208: OK 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 2.501s +202: Ran 6 tests in 4.973s 202: 202: OK -123: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +208: . +208: ---------------------------------------------------------------------- +208: Ran 1 test in 0.109s +208: +208: OK +208: ....... +208: ---------------------------------------------------------------------- +208: Ran 7 tests in 0.595s +208: +208: OK 202: ...EE.. 202: ====================================================================== 202: ERROR: testPerm1 (__main__.TestCase.testPerm1) @@ -39802,39 +40022,50 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 7 tests in 0.292s +202: Ran 7 tests in 0.222s 202: 202: FAILED (errors=2) 202: !!! TEST FAILURE: python UnitTestPackage.py {} +208: ... +208: ---------------------------------------------------------------------- +208: Ran 3 tests in 0.581s +208: +208: OK 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.034s +202: Ran 4 tests in 0.110s 202: 202: OK -123: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 -123: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 -123: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 -123: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 +123: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O +208: .ss.ss....... +208: ---------------------------------------------------------------------- +208: Ran 13 tests in 11.878s +208: +208: OK (skipped=4) +208: [18:40:38] Molecule does not have explicit Hs. Consider calling AddHs() +208: .[18:40:38] Molecule does not have explicit Hs. Consider calling AddHs() +123: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 +123: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 +123: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 12.162s +202: Ran 5 tests in 27.784s 202: 202: OK +123: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.006s +202: Ran 4 tests in 0.025s 202: 202: OK -123: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.002s +202: Ran 4 tests in 0.014s 202: 202: OK -123: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.016s +202: Ran 4 tests in 0.034s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestBuildComposite.py {} @@ -39845,7 +40076,7 @@ 202: !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} 202: !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'} 202: !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -200/208 Test #202: pythonTestDirML ........................***Failed 54.26 sec +205/208 Test #202: pythonTestDirML ........................***Failed 119.62 sec EEEEEEE ====================================================================== ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -39967,7 +40198,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 7 tests in 0.235s +Ran 7 tests in 0.771s FAILED (errors=7) EEEEEEEEEEEE @@ -40176,7 +40407,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 12 tests in 0.171s +Ran 12 tests in 0.726s FAILED (errors=12) Traceback (most recent call last): @@ -40202,22 +40433,22 @@ AssertionError: 0 is not true ---------------------------------------------------------------------- -Ran 1 test in 0.093s +Ran 1 test in 0.363s FAILED (failures=1) ... ---------------------------------------------------------------------- -Ran 3 tests in 0.005s +Ran 3 tests in 0.016s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.002s +Ran 8 tests in 0.014s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.603s +Ran 4 tests in 1.488s OK E.EEE @@ -40278,7 +40509,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 5 tests in 0.013s +Ran 5 tests in 0.037s FAILED (errors=4) .......E. @@ -40293,17 +40524,17 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 9 tests in 0.031s +Ran 9 tests in 0.052s FAILED (errors=1) ............ ---------------------------------------------------------------------- -Ran 12 tests in 0.017s +Ran 12 tests in 0.027s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.111s +Ran 5 tests in 0.197s OK ********************************************************************** @@ -40509,22 +40740,22 @@ OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.007s +Ran 6 tests in 0.012s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 1.149s +Ran 4 tests in 1.819s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.132s +Ran 6 tests in 0.180s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.648s +Ran 2 tests in 1.214s OK ........E. @@ -40543,18 +40774,18 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 10 tests in 0.035s +Ran 10 tests in 0.123s FAILED (errors=1) ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.529s +Ran 5 tests in 0.714s OK !!! TEST FAILURE: python UnitTestQuantTree.py {} .. ---------------------------------------------------------------------- -Ran 2 tests in 0.013s +Ran 2 tests in 0.033s OK ....Traceback (most recent call last): @@ -40583,12 +40814,12 @@ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- -Ran 5 tests in 0.087s +Ran 5 tests in 0.132s FAILED (errors=1) ... ---------------------------------------------------------------------- -Ran 3 tests in 0.063s +Ran 3 tests in 0.102s OK !!! TEST FAILURE: python UnitTestMolDescriptors.py {} @@ -40618,13 +40849,13 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 3 tests in 0.014s +Ran 3 tests in 0.020s FAILED (errors=3) !!! TEST FAILURE: python UnitTestCorrMatGen.py {} ...... ---------------------------------------------------------------------- -Ran 6 tests in 2.501s +Ran 6 tests in 4.973s OK ...EE.. @@ -40645,33 +40876,33 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 7 tests in 0.292s +Ran 7 tests in 0.222s FAILED (errors=2) !!! TEST FAILURE: python UnitTestPackage.py {} .... ---------------------------------------------------------------------- -Ran 4 tests in 0.034s +Ran 4 tests in 0.110s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 12.162s +Ran 5 tests in 27.784s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.006s +Ran 4 tests in 0.025s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.002s +Ran 4 tests in 0.014s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.016s +Ran 4 tests in 0.034s OK !!! TEST FAILURE: python UnitTestBuildComposite.py {} @@ -40683,307 +40914,113 @@ !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'} !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -test 203 - Start 203: pythonTestDirDataStructs - -203: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/DataStructs" -203: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit -203: Test timeout computed to be: 1500 -203: ....... -203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.068s -203: -203: OK -203: ............../build/reproducible-path/rdkit-202209.3/rdkit/DataStructs/UnitTestcBitVect.py:42: DeprecationWarning: Please use assertRaisesRegex instead. -203: with self.assertRaisesRegexp(IndexError, ""): -203: .................... -203: ---------------------------------------------------------------------- -203: Ran 34 tests in 0.021s -203: -203: OK -200: .........[10:31:34] INFO: Reading molecules and constructing molecular database. +200: .........[18:41:02] INFO: Reading molecules and constructing molecular database. 200: -200: [10:31:34] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [18:41:02] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [10:31:34] INFO: Processing 10 molecules +200: [18:41:02] INFO: Processing 10 molecules 200: -200: [10:31:34] INFO: Generating fingerprints and descriptors: +200: [18:41:03] INFO: Generating fingerprints and descriptors: 200: -200: [10:31:34] INFO: Finished. +200: [18:41:03] INFO: Finished. 200: -203: ..... -203: ---------------------------------------------------------------------- -203: Ran 5 tests in 0.090s -203: -203: OK -203: ....... -203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.006s -203: -203: OK -201/208 Test #203: pythonTestDirDataStructs ............... Passed 3.65 sec -test 204 - Start 204: pythonTestDirDbase - -204: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/Dbase" -204: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit -204: Test timeout computed to be: 1500 -204: .. -204: ---------------------------------------------------------------------- -204: Ran 2 tests in 0.093s -204: -204: OK -200: [10:31:36] INFO: Reading molecules and constructing molecular database. +123: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 +200: [18:41:09] INFO: Reading molecules and constructing molecular database. 200: -200: [10:31:36] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [18:41:09] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [10:31:36] INFO: Processing 10 molecules +200: [18:41:09] INFO: Processing 10 molecules 200: -200: [10:31:36] INFO: Generating fingerprints and descriptors: +200: [18:41:09] INFO: Generating fingerprints and descriptors: 200: -200: [10:31:36] INFO: Finished. +200: [18:41:09] INFO: Finished. 200: -204: ........... -204: ---------------------------------------------------------------------- -204: Ran 11 tests in 0.264s -204: -204: OK -204: . -204: ---------------------------------------------------------------------- -204: Ran 1 test in 0.004s -204: -204: OK -204: ../build/reproducible-path/rdkit-202209.3/rdkit/Dbase/UnitTestDbUtils.py:96: DeprecationWarning: Please use assertRaisesRegex instead. -204: with self.assertRaisesRegexp(IndexError, ""): -204: ............. -204: ---------------------------------------------------------------------- -204: Ran 15 tests in 0.122s -204: -204: OK -204: ...... -204: ---------------------------------------------------------------------- -204: Ran 6 tests in 0.015s -204: -204: OK -202/208 Test #204: pythonTestDirDbase ..................... Passed 2.54 sec -test 205 - Start 205: pythonTestDirSimDivFilters - -205: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/SimDivFilters" -205: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit -205: Test timeout computed to be: 1500 -123: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 -200: [10:31:39] INFO: Reading molecules and constructing molecular database. +123: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O +200: [18:41:15] INFO: Reading molecules and constructing molecular database. 200: -200: [10:31:39] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [18:41:15] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [10:31:39] INFO: Processing 10 molecules +200: [18:41:15] INFO: Processing 10 molecules 200: -200: [10:31:39] INFO: Generating fingerprints and descriptors: +200: [18:41:15] INFO: Generating fingerprints and descriptors: 200: -200: [10:31:39] INFO: Finished. +200: [18:41:15] INFO: Finished. 200: -203/208 Test #205: pythonTestDirSimDivFilters ............. Passed 1.10 sec -test 206 - Start 206: pythonTestDirVLib - -206: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/VLib" -206: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit -206: Test timeout computed to be: 1500 -123: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -206: ............. -206: ---------------------------------------------------------------------- -206: Ran 13 tests in 0.036s -206: -206: OK -206: ........... -206: ---------------------------------------------------------------------- -206: Ran 11 tests in 0.140s -206: -206: OK -200: [10:31:41] INFO: Reading molecules and constructing molecular database. +200: [18:41:21] INFO: Reading molecules and constructing molecular database. 200: -200: [10:31:41] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [18:41:21] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -204/208 Test #206: pythonTestDirVLib ...................... Passed 1.80 sec -test 207 - Start 207: pythonTestSping - -207: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/sping" -207: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit -207: Test timeout computed to be: 1500 -200: [10:31:41] INFO: Generating fingerprints and descriptors: +200: [18:41:22] INFO: Generating fingerprints and descriptors: 200: -200: [10:31:41] INFO: Finished. +200: [18:41:22] INFO: Finished. 200: -207: .. -207: ---------------------------------------------------------------------- -207: Ran 2 tests in 0.664s -207: -207: OK -205/208 Test #207: pythonTestSping ........................ Passed 2.09 sec -test 208 - Start 208: pythonTestDirChem - -208: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202209.3/rdkit/Chem" "--buildType" "None" -208: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem -208: Test timeout computed to be: 1500 -200: [10:31:43] INFO: Reading molecules and constructing molecular database. +123: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O +200: [18:41:28] INFO: Reading molecules and constructing molecular database. 200: -200: [10:31:43] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [18:41:28] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [10:31:43] INFO: Generating fingerprints and descriptors: +200: [18:41:28] INFO: Generating fingerprints and descriptors: 200: -200: [10:31:43] INFO: Finished. +200: [18:41:29] INFO: Finished. 200: -208: ....... -208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.320s -208: -208: OK -208: ...... -208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.146s -208: -208: OK -200: .[10:31:46] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. +123: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +200: .[18:41:35] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 200: -200: [10:31:46] INFO: Reading molecules and constructing molecular database. +200: [18:41:35] INFO: Reading molecules and constructing molecular database. 200: -200: [10:31:46] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [18:41:35] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [10:31:46] INFO: Processing 163 molecules +200: [18:41:35] INFO: Processing 163 molecules 200: -200: [10:31:46] INFO: done 100 +200: [18:41:36] INFO: done 100 200: -200: [10:31:47] INFO: Generating fingerprints and descriptors: +200: [18:41:37] INFO: Generating fingerprints and descriptors: 200: -208: ....[10:31:47] -208: -208: **** -208: Pre-condition Violation -208: valence not defined for atoms not associated with molecules -208: Violation occurred on line 422 in file ./Code/GraphMol/Atom.cpp -208: Failed Expression: dp_mol -208: **** -208: -208: . -208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.033s -208: -208: OK -208: .... -208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.038s -208: -208: OK -200: [10:31:48] INFO: Finished. +200: [18:41:39] INFO: Finished. 200: -208: .. -208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.047s -208: -208: OK -208: ...................... -208: ---------------------------------------------------------------------- -208: Ran 22 tests in 0.215s -208: -208: OK -208: .....s..........E......ss -208: ====================================================================== -208: ERROR: testIpc (__main__.TestCase.testIpc) -208: ---------------------------------------------------------------------- -208: Traceback (most recent call last): -208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestGraphDescriptors_2.py", line 112, in testIpc -208: Ipc = GraphDescriptors.Ipc(m, forceDMat=1) -208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -208: File "/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem/GraphDescriptors.py", line 124, in Ipc -208: cPoly = abs(Graphs.CharacteristicPolynomial(mol, adjMat)) -208: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ -208: File "/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem/Graphs.py", line 43, in CharacteristicPolynomial -208: res = numpy.zeros(nAtoms + 1, numpy.float) -208: ^^^^^^^^^^^ -208: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ -208: raise AttributeError(__former_attrs__[attr]) -208: AttributeError: module 'numpy' has no attribute 'float'. -208: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. -208: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: -208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -208: -208: ---------------------------------------------------------------------- -208: Ran 25 tests in 0.464s -208: -208: FAILED (errors=1, skipped=3) -200: .[10:31:53] INFO: Reading molecules and constructing molecular database. +123: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +200: .[18:41:51] INFO: Reading molecules and constructing molecular database. 200: -200: [10:31:53] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [18:41:51] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [10:31:53] INFO: Processing 10 molecules +200: [18:41:51] INFO: Processing 10 molecules 200: -200: [10:31:53] INFO: Generating fingerprints and descriptors: +200: [18:41:52] INFO: Generating fingerprints and descriptors: 200: -208: ..s -208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.649s -208: -208: OK (skipped=1) -200: [10:31:54] INFO: Finished. +200: [18:41:53] INFO: Finished. 200: -208: ................................... -208: ---------------------------------------------------------------------- -208: Ran 35 tests in 1.110s -208: -208: OK -200: [10:31:56] INFO: Reading molecules and constructing molecular database. +123: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 +200: [18:41:59] INFO: Reading molecules and constructing molecular database. 200: -200: [10:31:56] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [18:41:59] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [10:31:56] INFO: Processing 10 molecules +200: [18:41:59] INFO: Processing 10 molecules 200: -200: [10:31:57] INFO: Generating fingerprints and descriptors: +200: [18:42:00] INFO: Generating fingerprints and descriptors: 200: -208: .... -208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.102s -208: -208: OK -200: [10:31:58] INFO: Finished. +200: [18:42:01] INFO: Finished. 200: 200: . 200: ---------------------------------------------------------------------- -200: Ran 12 tests in 83.549s +200: Ran 12 tests in 183.633s 200: 200: OK -208: . -208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.036s -208: -208: OK -206/208 Test #200: pythonTestDbCLI ........................ Passed 84.25 sec -208: ....... -208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.141s -208: -208: OK -208: ... -208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.152s -208: -208: OK -208: .ss.ss....... -208: ---------------------------------------------------------------------- -208: Ran 13 tests in 3.571s -208: -208: OK (skipped=4) -208: [10:32:05] Molecule does not have explicit Hs. Consider calling AddHs() -208: .[10:32:05] Molecule does not have explicit Hs. Consider calling AddHs() -123: [10:32:08] Molecule does not have explicit Hs. Consider calling AddHs() -207/208 Test #123: testDistGeomHelpers .................... Passed 519.98 sec -208: .........F........[10:33:27] WARNING: More than one matching pattern found - picking one +206/208 Test #200: pythonTestDbCLI ........................ Passed 185.54 sec +123: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 +123: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 +123: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 +123: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 +123: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 +123: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 +123: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 +123: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] +123: [18:44:04] Molecule does not have explicit Hs. Consider calling AddHs() +207/208 Test #123: testDistGeomHelpers .................... Passed 1040.77 sec +208: .........F........[18:45:23] WARNING: More than one matching pattern found - picking one 208: -208: [10:33:28] WARNING: More than one matching pattern found - picking one +208: [18:45:23] WARNING: More than one matching pattern found - picking one 208: -208: .[10:33:28] WARNING: More than one matching pattern found - picking one +208: .[18:45:23] WARNING: More than one matching pattern found - picking one 208: 208: ... 208: ====================================================================== @@ -40993,19 +41030,19 @@ 208: File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestMol3D.py", line 244, in testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable 208: self.assertEqual(smiles, expected) 208: AssertionError: Items in the first set but not the second: -208: 'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I' 208: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@@H](N)I' +208: 'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I' 208: Items in the second set but not the first: -208: 'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@H](N)I' 208: 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@H](N)I' +208: 'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@H](N)I' 208: 208: ---------------------------------------------------------------------- -208: Ran 23 tests in 90.555s +208: Ran 23 tests in 309.821s 208: 208: FAILED (failures=1) -208: {'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl'} -208: {'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl'} -208: {'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} +208: {'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl'} +208: {'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl'} +208: {'F[C@H](Cl)[C@@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} 208: .....E.. 208: ====================================================================== 208: ERROR: test7ScoreMolecules (__main__.TestCase.test7ScoreMolecules) @@ -41025,7 +41062,7 @@ 208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 208: 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.232s +208: Ran 8 tests in 1.114s 208: 208: FAILED (errors=1) 208: Traceback (most recent call last): @@ -41060,10 +41097,10 @@ 208: `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. 208: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: 208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -208: F..[10:33:44] WARNING: not removing hydrogen atom without neighbors -208: [10:33:44] WARNING: not removing hydrogen atom without neighbors -208: [10:33:44] WARNING: not removing hydrogen atom without neighbors -208: ....[10:33:44] WARNING: not removing hydrogen atom without neighbors +208: F..[18:46:24] WARNING: not removing hydrogen atom without neighbors +208: [18:46:24] WARNING: not removing hydrogen atom without neighbors +208: [18:46:24] WARNING: not removing hydrogen atom without neighbors +208: ....[18:46:25] WARNING: not removing hydrogen atom without neighbors 208: ...... 208: ====================================================================== 208: FAIL: testBadAtomHandling (__main__.TestCase.testBadAtomHandling) @@ -41120,17 +41157,17 @@ 208: AssertionError: SMILES: CCC; Descriptor: Ipc 208: 208: ---------------------------------------------------------------------- -208: Ran 14 tests in 7.123s +208: Ran 14 tests in 30.792s 208: 208: FAILED (failures=2) 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 3.034s +208: Ran 4 tests in 12.543s 208: 208: OK 208: ...... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.787s +208: Ran 6 tests in 3.284s 208: 208: OK 208: .......:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. @@ -41141,17 +41178,17 @@ 208: antibiotics = antibiotics.append({ 208: .......s..s........ 208: ---------------------------------------------------------------------- -208: Ran 26 tests in 6.130s +208: Ran 26 tests in 21.582s 208: 208: OK (skipped=2) -208: .............F[10:34:26] WARNING: More than one matching pattern found - picking one +208: .............F[18:48:48] WARNING: More than one matching pattern found - picking one 208: -208: [10:34:26] WARNING: More than one matching pattern found - picking one +208: [18:48:48] WARNING: More than one matching pattern found - picking one 208: -208: ..[10:34:27] Molecule does not have explicit Hs. Consider calling AddHs() -208: [10:34:27] Molecule does not have explicit Hs. Consider calling AddHs() -208: [10:34:27] Molecule does not have explicit Hs. Consider calling AddHs() -208: [10:34:27] Molecule does not have explicit Hs. Consider calling AddHs() +208: ..[18:48:49] Molecule does not have explicit Hs. Consider calling AddHs() +208: [18:48:49] Molecule does not have explicit Hs. Consider calling AddHs() +208: [18:48:49] Molecule does not have explicit Hs. Consider calling AddHs() +208: [18:48:49] Molecule does not have explicit Hs. Consider calling AddHs() 208: ......... 208: ====================================================================== 208: FAIL: FindBRICSBonds (rdkit.Chem.BRICS) @@ -41180,285 +41217,285 @@ 208: 208: 208: ---------------------------------------------------------------------- -208: Ran 25 tests in 26.634s +208: Ran 25 tests in 85.651s 208: 208: FAILED (failures=1) 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.123s +208: Ran 2 tests in 0.432s 208: 208: OK 208: ..s... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 2.306s +208: Ran 6 tests in 6.700s 208: 208: OK (skipped=1) -208: ..[10:34:31] WARNING: not removing hydrogen atom without neighbors -208: .[10:34:31] WARNING: not removing hydrogen atom without neighbors -208: .[10:34:31] WARNING: no name column found on line 1 -208: [10:34:31] WARNING: no name column found on line 2 -208: [10:34:31] WARNING: no name column found on line 3 -208: [10:34:31] WARNING: no name column found on line 4 -208: [10:34:31] WARNING: no name column found on line 5 -208: [10:34:31] WARNING: no name column found on line 6 -208: [10:34:31] WARNING: no name column found on line 7 -208: [10:34:31] WARNING: no name column found on line 8 -208: [10:34:31] WARNING: no name column found on line 9 -208: [10:34:31] WARNING: no name column found on line 10 -208: [10:34:31] WARNING: no name column found on line 11 -208: [10:34:31] WARNING: no name column found on line 12 -208: [10:34:31] WARNING: no name column found on line 13 -208: [10:34:31] WARNING: no name column found on line 14 -208: [10:34:31] WARNING: no name column found on line 15 -208: [10:34:31] WARNING: no name column found on line 16 -208: [10:34:31] WARNING: no name column found on line 17 -208: [10:34:31] WARNING: no name column found on line 18 -208: [10:34:31] WARNING: no name column found on line 19 -208: [10:34:31] WARNING: no name column found on line 20 -208: 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WARNING: no name column found on line 38 -208: [10:34:31] WARNING: no name column found on line 39 -208: [10:34:31] WARNING: no name column found on line 40 -208: [10:34:31] WARNING: no name column found on line 41 -208: [10:34:31] WARNING: no name column found on line 42 -208: [10:34:31] WARNING: no name column found on line 43 -208: [10:34:31] WARNING: no name column found on line 44 -208: [10:34:31] WARNING: no name column found on line 45 -208: [10:34:31] WARNING: no name column found on line 46 -208: [10:34:31] WARNING: no name column found on line 47 -208: [10:34:31] WARNING: no name column found on line 48 -208: [10:34:31] WARNING: no name column found on line 49 -208: [10:34:31] WARNING: no name column found on line 50 -208: [10:34:31] WARNING: no name column found on line 51 -208: [10:34:31] WARNING: no name column found on line 52 -208: [10:34:31] WARNING: no name column found on line 53 -208: [10:34:31] WARNING: no name column found on line 54 -208: [10:34:31] WARNING: no 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line 140 -208: [10:34:31] WARNING: no name column found on line 141 -208: [10:34:31] WARNING: no name column found on line 142 -208: [10:34:31] WARNING: no name column found on line 143 -208: [10:34:31] WARNING: no name column found on line 144 -208: [10:34:31] WARNING: no name column found on line 145 -208: [10:34:31] WARNING: no name column found on line 146 -208: [10:34:31] WARNING: no name column found on line 147 -208: [10:34:31] WARNING: no name column found on line 148 -208: [10:34:31] WARNING: no name column found on line 149 -208: [10:34:31] WARNING: no name column found on line 150 -208: [10:34:31] WARNING: no name column found on line 151 -208: [10:34:31] WARNING: no name column found on line 152 -208: [10:34:31] WARNING: no name column found on line 153 -208: [10:34:31] WARNING: no name column found on line 154 -208: [10:34:31] WARNING: no name column found on line 155 -208: [10:34:31] WARNING: no name column found on line 156 -208: [10:34:31] WARNING: no name column found on line 157 -208: [10:34:31] WARNING: no name column found on line 158 -208: [10:34:31] WARNING: no name column found on line 159 -208: [10:34:31] WARNING: no name column found on line 160 -208: [10:34:31] WARNING: no name column found on line 161 -208: [10:34:31] WARNING: no name column found on line 162 -208: [10:34:31] WARNING: no name column found on line 163 -208: [10:34:31] WARNING: no name column found on line 164 -208: [10:34:31] WARNING: no name column found on line 165 -208: [10:34:31] WARNING: no name column found on line 166 -208: [10:34:31] WARNING: no name column found on line 167 -208: [10:34:31] WARNING: no name column found on line 168 -208: [10:34:31] WARNING: no name column found on line 169 -208: [10:34:31] WARNING: no name column found on line 170 -208: [10:34:31] WARNING: no name column found on line 171 -208: [10:34:31] WARNING: no name column found on line 172 -208: [10:34:31] WARNING: no name column found on line 173 -208: [10:34:31] WARNING: no name column found on line 174 -208: [10:34:31] WARNING: no name column found on line 175 -208: [10:34:31] WARNING: no name column found on line 176 -208: [10:34:31] WARNING: no name column found on line 177 -208: [10:34:31] WARNING: no name column found on line 178 -208: [10:34:31] WARNING: no name column found on line 179 -208: [10:34:31] WARNING: no name column found on line 180 -208: [10:34:31] WARNING: no name column found on line 181 -208: [10:34:31] WARNING: no name column found on line 182 -208: [10:34:31] WARNING: no name column found on line 183 -208: [10:34:31] WARNING: no name column found on line 184 -208: [10:34:31] WARNING: no name column found on line 185 -208: [10:34:31] WARNING: no name column found on line 186 -208: [10:34:31] WARNING: no name column found on line 187 -208: [10:34:31] WARNING: no name column found on line 188 -208: [10:34:31] WARNING: no name column found on line 189 -208: [10:34:31] WARNING: no name column found on line 190 -208: [10:34:31] WARNING: no name column found on line 191 -208: [10:34:31] WARNING: no name column found on line 192 -208: [10:34:31] WARNING: no name column found on line 193 -208: [10:34:31] WARNING: no name column found on line 194 -208: [10:34:31] WARNING: no name column found on line 195 -208: [10:34:31] WARNING: no name column found on line 196 -208: [10:34:31] WARNING: no name column found on line 197 -208: [10:34:31] WARNING: no name column found on line 198 -208: [10:34:31] WARNING: no name column found on line 199 -208: [10:34:31] WARNING: no name column found on line 200 -208: [10:34:31] WARNING: no name column found on line 201 -208: [10:34:31] WARNING: no name column found on line 202 -208: [10:34:31] WARNING: no name column found on line 203 -208: [10:34:31] WARNING: no name column found on line 204 -208: [10:34:31] WARNING: no name column found on line 205 -208: [10:34:31] WARNING: no name column found on line 206 -208: [10:34:31] WARNING: no name column found on line 207 -208: [10:34:31] WARNING: no name column found on line 208 -208: [10:34:31] WARNING: no name column found on line 209 -208: [10:34:31] WARNING: no name column found on line 210 -208: [10:34:31] WARNING: no name column found on line 211 -208: [10:34:31] WARNING: no name column found on line 212 -208: [10:34:31] WARNING: no name column found on line 213 -208: [10:34:31] WARNING: no name column found on line 214 -208: [10:34:31] WARNING: no name column found on line 215 -208: [10:34:31] WARNING: no name column found on line 216 +208: ..[18:49:03] WARNING: not removing hydrogen atom without neighbors +208: .[18:49:03] WARNING: not removing hydrogen atom without neighbors +208: .[18:49:04] WARNING: no name column found on line 1 +208: [18:49:04] WARNING: no name column found on line 2 +208: [18:49:04] WARNING: no name column found on line 3 +208: [18:49:04] WARNING: no name column found on line 4 +208: [18:49:04] WARNING: no name column found on line 5 +208: [18:49:04] WARNING: no name column found on line 6 +208: [18:49:04] WARNING: no name column found on line 7 +208: [18:49:04] WARNING: no name column found on line 8 +208: [18:49:04] WARNING: no name column found on line 9 +208: [18:49:04] WARNING: no name column found on line 10 +208: [18:49:04] WARNING: no name column found on line 11 +208: [18:49:04] WARNING: no name column found on line 12 +208: [18:49:04] WARNING: no name column found on line 13 +208: [18:49:04] WARNING: no name column found on line 14 +208: [18:49:04] WARNING: no name column found on line 15 +208: [18:49:04] WARNING: no name column found on line 16 +208: [18:49:04] WARNING: no name column found on line 17 +208: [18:49:04] WARNING: no name column found on line 18 +208: [18:49:04] WARNING: no name column found on line 19 +208: [18:49:04] WARNING: no name column found on line 20 +208: [18:49:04] WARNING: no name column found on line 21 +208: [18:49:04] WARNING: no name column found on line 22 +208: [18:49:04] WARNING: no name column found on line 23 +208: [18:49:04] WARNING: no name column found on line 24 +208: [18:49:04] WARNING: no name column found on line 25 +208: [18:49:04] WARNING: no name column found on line 26 +208: [18:49:04] WARNING: no name column found on line 27 +208: [18:49:04] WARNING: no name column found on line 28 +208: [18:49:04] WARNING: no name column found on line 29 +208: [18:49:04] WARNING: no name column found on line 30 +208: [18:49:04] WARNING: no name column found on line 31 +208: [18:49:04] WARNING: no name column found on line 32 +208: [18:49:04] WARNING: no name column found on line 33 +208: [18:49:04] WARNING: no name column found on line 34 +208: [18:49:04] WARNING: no name column found on line 35 +208: [18:49:04] WARNING: no name column found on line 36 +208: [18:49:04] WARNING: no name column found on line 37 +208: [18:49:04] WARNING: no name column found on line 38 +208: [18:49:04] WARNING: no name column found on line 39 +208: [18:49:04] WARNING: no name column found on line 40 +208: [18:49:04] WARNING: no name column found on line 41 +208: [18:49:04] WARNING: no name column found on line 42 +208: [18:49:04] WARNING: no name column found on line 43 +208: [18:49:04] WARNING: no name column found on line 44 +208: [18:49:04] WARNING: no name column found on line 45 +208: [18:49:04] WARNING: no name column found on line 46 +208: [18:49:04] WARNING: no name column found on line 47 +208: [18:49:04] WARNING: no name column found on line 48 +208: [18:49:04] WARNING: no name column found on line 49 +208: [18:49:04] WARNING: no name column found on line 50 +208: [18:49:04] WARNING: no name column found on line 51 +208: [18:49:04] WARNING: no name column found on line 52 +208: [18:49:04] WARNING: no name column found on line 53 +208: [18:49:04] WARNING: no name column found on line 54 +208: [18:49:04] WARNING: no name column found on line 55 +208: [18:49:04] WARNING: no name column found on line 56 +208: [18:49:04] WARNING: no name column found on line 57 +208: [18:49:04] WARNING: no name column found on line 58 +208: [18:49:04] WARNING: no name column found on line 59 +208: [18:49:04] WARNING: no name column found on line 60 +208: [18:49:04] WARNING: no name column found on line 61 +208: [18:49:04] WARNING: no name column found on line 62 +208: [18:49:04] WARNING: no name column found on line 63 +208: [18:49:04] WARNING: no name column found on line 64 +208: [18:49:04] WARNING: no name column found on line 65 +208: [18:49:04] WARNING: no name column found on line 66 +208: [18:49:04] WARNING: no name column found on line 67 +208: [18:49:04] WARNING: no name column found on line 68 +208: [18:49:04] WARNING: no name column found on line 69 +208: [18:49:04] WARNING: no name column found on line 70 +208: [18:49:04] WARNING: no name column found on line 71 +208: [18:49:04] WARNING: no name column found on line 72 +208: [18:49:04] WARNING: no name column found on line 73 +208: [18:49:04] WARNING: no name column found on line 74 +208: [18:49:04] WARNING: no name column found on line 75 +208: [18:49:04] WARNING: no name column found on line 76 +208: [18:49:04] WARNING: no name column found on line 77 +208: [18:49:04] WARNING: no name column found on line 78 +208: [18:49:04] WARNING: no name column found on line 79 +208: [18:49:04] WARNING: no name column found on line 80 +208: [18:49:04] WARNING: no name column found on line 81 +208: [18:49:04] WARNING: no name column found on line 82 +208: [18:49:04] WARNING: no name column found on line 83 +208: [18:49:04] WARNING: no name column found on line 84 +208: [18:49:04] WARNING: no name column found on line 85 +208: [18:49:04] WARNING: no name column found on line 86 +208: [18:49:04] WARNING: no name column found on line 87 +208: [18:49:04] WARNING: no name column found on line 88 +208: [18:49:04] WARNING: no name column found on line 89 +208: [18:49:04] WARNING: no name column found on line 90 +208: [18:49:04] WARNING: no name column found on line 91 +208: [18:49:04] WARNING: no name column found on line 92 +208: 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[18:49:04] WARNING: no name column found on line 110 +208: [18:49:04] WARNING: no name column found on line 111 +208: [18:49:04] WARNING: no name column found on line 112 +208: [18:49:04] WARNING: no name column found on line 113 +208: [18:49:04] WARNING: no name column found on line 114 +208: [18:49:04] WARNING: no name column found on line 115 +208: [18:49:04] WARNING: no name column found on line 116 +208: [18:49:04] WARNING: no name column found on line 117 +208: [18:49:04] WARNING: no name column found on line 118 +208: [18:49:04] WARNING: no name column found on line 119 +208: [18:49:04] WARNING: no name column found on line 120 +208: [18:49:04] WARNING: no name column found on line 121 +208: [18:49:04] WARNING: no name column found on line 122 +208: [18:49:04] WARNING: no name column found on line 123 +208: [18:49:04] WARNING: no name column found on line 124 +208: [18:49:04] WARNING: no name column found on line 125 +208: [18:49:04] WARNING: no name column found on line 126 +208: [18:49:04] WARNING: no name column found on line 127 +208: [18:49:04] WARNING: no name column found on line 128 +208: [18:49:04] WARNING: no name column found on line 129 +208: [18:49:04] WARNING: no name column found on line 130 +208: [18:49:04] WARNING: no name column found on line 131 +208: [18:49:04] WARNING: no name column found on line 132 +208: [18:49:04] WARNING: no name column found on line 133 +208: [18:49:04] WARNING: no name column found on line 134 +208: [18:49:04] WARNING: no name column found on line 135 +208: [18:49:04] WARNING: no name column found on line 136 +208: [18:49:04] WARNING: no name column found on line 137 +208: [18:49:04] WARNING: no name column found on line 138 +208: [18:49:04] WARNING: no name column found on line 139 +208: [18:49:04] WARNING: no name column found on line 140 +208: [18:49:04] WARNING: no name column found on line 141 +208: [18:49:04] WARNING: no name column found on line 142 +208: [18:49:04] WARNING: no name column found on line 143 +208: [18:49:04] WARNING: no name column found on line 144 +208: [18:49:04] WARNING: no name column found on line 145 +208: [18:49:04] WARNING: no name column found on line 146 +208: [18:49:04] WARNING: no name column found on line 147 +208: [18:49:04] WARNING: no name column found on line 148 +208: [18:49:04] WARNING: no name column found on line 149 +208: [18:49:04] WARNING: no name column found on line 150 +208: [18:49:04] WARNING: no name column found on line 151 +208: [18:49:04] WARNING: no name column found on line 152 +208: [18:49:04] WARNING: no name column found on line 153 +208: [18:49:04] WARNING: no name column found on line 154 +208: [18:49:04] WARNING: no name column found on line 155 +208: [18:49:04] WARNING: no name column found on line 156 +208: [18:49:04] WARNING: no name column found on line 157 +208: [18:49:04] WARNING: no name column found on line 158 +208: [18:49:04] WARNING: no name column found on line 159 +208: [18:49:04] WARNING: no name column found on line 160 +208: [18:49:04] WARNING: no name column found on line 161 +208: [18:49:04] WARNING: no name column found on line 162 +208: [18:49:04] WARNING: no name column found on line 163 +208: [18:49:04] WARNING: no name column found on line 164 +208: [18:49:04] WARNING: no name column found on line 165 +208: [18:49:04] WARNING: no name column found on line 166 +208: [18:49:04] WARNING: no name column found on line 167 +208: [18:49:04] WARNING: no name column found on line 168 +208: [18:49:04] WARNING: no name column found on line 169 +208: [18:49:04] WARNING: no name column found on line 170 +208: [18:49:04] WARNING: no name column found on line 171 +208: [18:49:04] WARNING: no name column found on line 172 +208: [18:49:04] WARNING: no name column found on line 173 +208: [18:49:04] WARNING: no name column found on line 174 +208: [18:49:04] WARNING: no name column found on line 175 +208: [18:49:04] WARNING: no name column found on line 176 +208: [18:49:04] WARNING: no name column found on line 177 +208: [18:49:04] WARNING: no name column found on line 178 +208: [18:49:04] WARNING: no name column found on line 179 +208: [18:49:04] WARNING: no name column found on line 180 +208: [18:49:04] WARNING: no name column found on line 181 +208: [18:49:04] WARNING: no name column found on line 182 +208: [18:49:04] WARNING: no name column found on line 183 +208: [18:49:04] WARNING: no name column found on line 184 +208: [18:49:04] WARNING: no name column found on line 185 +208: [18:49:04] WARNING: no name column found on line 186 +208: [18:49:04] WARNING: no name column found on line 187 +208: [18:49:04] WARNING: no name column found on line 188 +208: [18:49:04] WARNING: no name column found on line 189 +208: [18:49:04] WARNING: no name column found on line 190 +208: [18:49:04] WARNING: no name column found on line 191 +208: [18:49:04] WARNING: no name column found on line 192 +208: [18:49:04] WARNING: no name column found on line 193 +208: [18:49:04] WARNING: no name column found on line 194 +208: [18:49:04] WARNING: no name column found on line 195 +208: [18:49:04] WARNING: no name column found on line 196 +208: [18:49:04] WARNING: no name column found on line 197 +208: [18:49:04] WARNING: no name column found on line 198 +208: [18:49:04] WARNING: no name column found on line 199 +208: [18:49:04] WARNING: no name column found on line 200 +208: [18:49:04] WARNING: no name column found on line 201 +208: [18:49:04] WARNING: no name column found on line 202 +208: [18:49:04] WARNING: no name column found on line 203 +208: [18:49:04] WARNING: no name column found on line 204 +208: [18:49:04] WARNING: no name column found on line 205 +208: [18:49:04] WARNING: no name column found on line 206 +208: [18:49:04] WARNING: no name column found on line 207 +208: [18:49:04] WARNING: no name column found on line 208 +208: [18:49:04] WARNING: no name column found on line 209 +208: [18:49:04] WARNING: no name column found on line 210 +208: [18:49:04] WARNING: no name column found on line 211 +208: [18:49:04] WARNING: no name column found on line 212 +208: [18:49:04] WARNING: no name column found on line 213 +208: [18:49:04] WARNING: no name column found on line 214 +208: [18:49:04] WARNING: no name column found on line 215 +208: [18:49:04] WARNING: no name column found on line 216 208: ...... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.308s +208: Ran 10 tests in 0.967s 208: 208: OK 208: .................. 208: ---------------------------------------------------------------------- -208: Ran 18 tests in 2.079s +208: Ran 18 tests in 8.659s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.213s +208: Ran 3 tests in 1.090s 208: 208: OK 208: ........ 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.078s +208: Ran 8 tests in 0.465s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.050s +208: Ran 2 tests in 0.247s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.039s +208: Ran 2 tests in 0.205s 208: 208: OK 208: . 208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.254s +208: Ran 1 test in 0.981s 208: 208: OK 208: ........ 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.004s +208: Ran 8 tests in 0.016s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.009s +208: Ran 3 tests in 0.052s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.004s +208: Ran 3 tests in 0.021s 208: 208: OK 208: ...E @@ -41480,28 +41517,28 @@ 208: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 208: 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.013s +208: Ran 4 tests in 0.056s 208: 208: FAILED (errors=1) 208: !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} 208: ....... 208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.038s +208: Ran 7 tests in 0.160s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.042s +208: Ran 4 tests in 0.205s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 7.814s +208: Ran 4 tests in 29.337s 208: 208: OK 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.137s +208: Ran 10 tests in 0.536s 208: 208: OK 208: . @@ -41511,7 +41548,7 @@ 208: OK 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.009s +208: Ran 10 tests in 0.048s 208: 208: OK 208: ....E @@ -41530,15 +41567,15 @@ 208: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 208: 208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.104s +208: Ran 5 tests in 0.350s 208: 208: FAILED (errors=1) 208: !!! TEST FAILURE: python UnitTestGobbi.py {} -208: ................[10:35:14] Molecule does not have explicit Hs. Consider calling AddHs() -208: [10:35:14] Molecule does not have explicit Hs. Consider calling AddHs() +208: ................[18:51:44] Molecule does not have explicit Hs. Consider calling AddHs() +208: [18:51:44] Molecule does not have explicit Hs. Consider calling AddHs() 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 21 tests in 17.441s +208: Ran 21 tests in 51.504s 208: 208: OK 208: mol_197 @@ -41549,10 +41586,10 @@ 208: 216.26,5.67,105.00,0.87,103.81,0.89,89.27,0.92,6.00 208: . 208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.001s +208: Ran 1 test in 0.009s 208: 208: OK -208: ...[10:35:16] +208: ...[18:51:48] 208: 208: **** 208: Pre-condition Violation @@ -41563,65 +41600,65 @@ 208: 208: . 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.052s +208: Ran 4 tests in 0.151s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 26.298s +208: Ran 2 tests in 87.565s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.251s +208: Ran 2 tests in 1.094s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.028s +208: Ran 3 tests in 0.093s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.056s +208: Ran 4 tests in 0.235s 208: 208: OK -208: .....[10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors -208: [10:35:47] WARNING: not removing hydrogen atom without neighbors +208: .....[18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors +208: [18:53:35] WARNING: not removing hydrogen atom without neighbors 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.822s +208: Ran 10 tests in 3.506s 208: 208: OK -208: ssssss[10:35:49] No suitable metadata found. -208: .[10:35:49] No suitable metadata found. +208: ssssss[18:53:43] No suitable metadata found. +208: .[18:53:43] No suitable metadata found. 208: ......s/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually 208: warnings.warn( 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 19 tests in 0.928s +208: Ran 19 tests in 4.288s 208: 208: OK (skipped=7) 208: sss. 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 1.640s +208: Ran 4 tests in 6.871s 208: 208: OK (skipped=3) 208: sss @@ -41631,33 +41668,33 @@ 208: OK (skipped=3) 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 1.653s +208: Ran 10 tests in 6.605s 208: 208: OK -208: ..[10:35:56] SMARTS Parse Error: syntax error while parsing: boromicacid -208: [10:35:56] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -208: [10:35:56] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -208: [10:35:56] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -208: [10:35:56] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -208: [10:35:56] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -208: [10:35:56] reaction has no reactants -208: [10:35:56] reaction has no products -208: [10:35:56] initialization failed -208: [10:35:56] reaction has no reactants -208: [10:35:56] reaction has no products +208: ..[18:54:14] SMARTS Parse Error: syntax error while parsing: boromicacid +208: [18:54:14] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +208: [18:54:14] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +208: [18:54:14] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +208: [18:54:14] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +208: [18:54:14] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +208: [18:54:14] reaction has no reactants +208: [18:54:14] reaction has no products +208: [18:54:14] initialization failed +208: [18:54:14] reaction has no reactants +208: [18:54:14] reaction has no products 208: . 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.069s +208: Ran 3 tests in 0.285s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.028s +208: Ran 4 tests in 0.119s 208: 208: OK 208: .................... 208: ---------------------------------------------------------------------- -208: Ran 20 tests in 0.299s +208: Ran 20 tests in 1.251s 208: 208: OK 208: !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} @@ -41667,18 +41704,18 @@ 208: !!! TEST FAILURE: python UnitTestDocTestsChem.py {} 208: !!! TEST FAILURE: python test_list.py {'dir': 'FeatMaps'} 208: !!! TEST FAILURE: python test_list.py {'dir': 'Pharm2D'} -208/208 Test #208: pythonTestDirChem ......................***Failed 255.46 sec +208/208 Test #208: pythonTestDirChem ......................***Failed 886.47 sec ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.320s +Ran 7 tests in 0.956s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.146s +Ran 6 tests in 0.166s OK -....[10:31:47] +....[18:39:49] **** Pre-condition Violation @@ -41689,22 +41726,22 @@ . ---------------------------------------------------------------------- -Ran 5 tests in 0.033s +Ran 5 tests in 0.085s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.038s +Ran 4 tests in 0.088s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.047s +Ran 2 tests in 0.089s OK ...................... ---------------------------------------------------------------------- -Ran 22 tests in 0.215s +Ran 22 tests in 0.334s OK .....s..........E......ss @@ -41729,51 +41766,51 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 25 tests in 0.464s +Ran 25 tests in 1.277s FAILED (errors=1, skipped=3) ..s ---------------------------------------------------------------------- -Ran 3 tests in 0.649s +Ran 3 tests in 1.464s OK (skipped=1) ................................... ---------------------------------------------------------------------- -Ran 35 tests in 1.110s +Ran 35 tests in 1.257s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.102s +Ran 4 tests in 0.166s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.036s +Ran 1 test in 0.109s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.141s +Ran 7 tests in 0.595s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.152s +Ran 3 tests in 0.581s OK .ss.ss....... ---------------------------------------------------------------------- -Ran 13 tests in 3.571s +Ran 13 tests in 11.878s OK (skipped=4) -[10:32:05] Molecule does not have explicit Hs. Consider calling AddHs() -.[10:32:05] Molecule does not have explicit Hs. Consider calling AddHs() -.........F........[10:33:27] WARNING: More than one matching pattern found - picking one +[18:40:38] Molecule does not have explicit Hs. Consider calling AddHs() +.[18:40:38] Molecule does not have explicit Hs. Consider calling AddHs() +.........F........[18:45:23] WARNING: More than one matching pattern found - picking one -[10:33:28] WARNING: More than one matching pattern found - picking one +[18:45:23] WARNING: More than one matching pattern found - picking one -.[10:33:28] WARNING: More than one matching pattern found - picking one +.[18:45:23] WARNING: More than one matching pattern found - picking one ... ====================================================================== @@ -41783,19 +41820,19 @@ File "/build/reproducible-path/rdkit-202209.3/rdkit/Chem/UnitTestMol3D.py", line 244, in testEnumerateStereoisomersRandomSamplingShouldBeDeterministicAndPortable self.assertEqual(smiles, expected) AssertionError: Items in the first set but not the second: -'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I' 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@@H](N)I' +'C/C(F)=C/[C@@H](Cl)/C=C(/Br)[C@@H](N)I' Items in the second set but not the first: -'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@H](N)I' 'C/C(F)=C/[C@@H](Cl)/C=C(\\Br)[C@H](N)I' +'C/C(F)=C\\[C@H](Cl)/C=C(\\Br)[C@H](N)I' ---------------------------------------------------------------------- -Ran 23 tests in 90.555s +Ran 23 tests in 309.821s FAILED (failures=1) -{'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl'} -{'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl'} -{'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} +{'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl'} +{'C/C(F)=C\\[C@H](C)Cl', 'C/C(F)=C\\[C@@H](C)Cl', 'C/C(F)=C/[C@@H](C)Cl', 'C/C(F)=C/[C@H](C)Cl'} +{'F[C@H](Cl)[C@@H](F)Cl', 'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl'} .....E.. ====================================================================== ERROR: test7ScoreMolecules (__main__.TestCase.test7ScoreMolecules) @@ -41815,7 +41852,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 8 tests in 0.232s +Ran 8 tests in 1.114s FAILED (errors=1) Traceback (most recent call last): @@ -41850,10 +41887,10 @@ `np.float` was a deprecated alias for the builtin `float`. To avoid this error in existing code, use `float` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.float64` here. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -F..[10:33:44] WARNING: not removing hydrogen atom without neighbors -[10:33:44] WARNING: not removing hydrogen atom without neighbors -[10:33:44] WARNING: not removing hydrogen atom without neighbors -....[10:33:44] WARNING: not removing hydrogen atom without neighbors +F..[18:46:24] WARNING: not removing hydrogen atom without neighbors +[18:46:24] WARNING: not removing hydrogen atom without neighbors +[18:46:24] WARNING: not removing hydrogen atom without neighbors +....[18:46:25] WARNING: not removing hydrogen atom without neighbors ...... ====================================================================== FAIL: testBadAtomHandling (__main__.TestCase.testBadAtomHandling) @@ -41910,17 +41947,17 @@ AssertionError: SMILES: CCC; Descriptor: Ipc ---------------------------------------------------------------------- -Ran 14 tests in 7.123s +Ran 14 tests in 30.792s FAILED (failures=2) .... ---------------------------------------------------------------------- -Ran 4 tests in 3.034s +Ran 4 tests in 12.543s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.787s +Ran 6 tests in 3.284s OK .......:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. @@ -41931,17 +41968,17 @@ antibiotics = antibiotics.append({ .......s..s........ ---------------------------------------------------------------------- -Ran 26 tests in 6.130s +Ran 26 tests in 21.582s OK (skipped=2) -.............F[10:34:26] WARNING: More than one matching pattern found - picking one +.............F[18:48:48] WARNING: More than one matching pattern found - picking one -[10:34:26] WARNING: More than one matching pattern found - picking one +[18:48:48] WARNING: More than one matching pattern found - picking one -..[10:34:27] Molecule does not have explicit Hs. Consider calling AddHs() -[10:34:27] Molecule does not have explicit Hs. Consider calling AddHs() -[10:34:27] Molecule does not have explicit Hs. Consider calling AddHs() -[10:34:27] Molecule does not have explicit Hs. Consider calling AddHs() +..[18:48:49] Molecule does not have explicit Hs. Consider calling AddHs() +[18:48:49] Molecule does not have explicit Hs. Consider calling AddHs() +[18:48:49] Molecule does not have explicit Hs. Consider calling AddHs() +[18:48:49] Molecule does not have explicit Hs. Consider calling AddHs() ......... ====================================================================== FAIL: FindBRICSBonds (rdkit.Chem.BRICS) @@ -41970,285 +42007,285 @@ ---------------------------------------------------------------------- -Ran 25 tests in 26.634s +Ran 25 tests in 85.651s FAILED (failures=1) .. ---------------------------------------------------------------------- -Ran 2 tests in 0.123s +Ran 2 tests in 0.432s OK ..s... ---------------------------------------------------------------------- -Ran 6 tests in 2.306s +Ran 6 tests in 6.700s OK (skipped=1) -..[10:34:31] WARNING: not removing hydrogen atom without neighbors -.[10:34:31] WARNING: not removing hydrogen atom without neighbors -.[10:34:31] WARNING: no name column found on line 1 -[10:34:31] WARNING: no name column found on line 2 -[10:34:31] WARNING: no name column found on line 3 -[10:34:31] WARNING: no name column found on line 4 -[10:34:31] WARNING: no name column found on line 5 -[10:34:31] WARNING: no name column found on line 6 -[10:34:31] WARNING: no name column found on line 7 -[10:34:31] WARNING: no name column found on line 8 -[10:34:31] WARNING: no name column found on line 9 -[10:34:31] WARNING: no name column found on line 10 -[10:34:31] WARNING: no name column found on line 11 -[10:34:31] WARNING: no name column found on line 12 -[10:34:31] WARNING: no name column found on line 13 -[10:34:31] WARNING: no name column found on line 14 -[10:34:31] WARNING: no name column found on line 15 -[10:34:31] WARNING: no name column found on line 16 -[10:34:31] WARNING: no name column found on line 17 -[10:34:31] WARNING: no name column found on line 18 -[10:34:31] WARNING: no name column found on line 19 -[10:34:31] WARNING: no name column found on line 20 -[10:34:31] WARNING: no name column found on line 21 -[10:34:31] WARNING: no name column found on line 22 -[10:34:31] WARNING: no name column found on line 23 -[10:34:31] WARNING: no name column found on line 24 -[10:34:31] WARNING: no name column found on line 25 -[10:34:31] WARNING: no name column found on line 26 -[10:34:31] WARNING: no name column found on line 27 -[10:34:31] WARNING: no name column found on line 28 -[10:34:31] WARNING: no name column found on line 29 -[10:34:31] WARNING: no name column found on line 30 -[10:34:31] WARNING: no name column found on line 31 -[10:34:31] WARNING: no name column found on line 32 -[10:34:31] WARNING: no name column found on line 33 -[10:34:31] WARNING: no name column found on line 34 -[10:34:31] WARNING: no name column found on line 35 -[10:34:31] WARNING: no name column found on line 36 -[10:34:31] WARNING: no name column found on line 37 -[10:34:31] WARNING: no name column found on line 38 -[10:34:31] WARNING: no name column found on line 39 -[10:34:31] WARNING: no name column found on line 40 -[10:34:31] WARNING: no name column found on line 41 -[10:34:31] WARNING: no name column found on line 42 -[10:34:31] WARNING: no name column found on line 43 -[10:34:31] 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found on line 100 -[10:34:31] WARNING: no name column found on line 101 -[10:34:31] WARNING: no name column found on line 102 -[10:34:31] WARNING: no name column found on line 103 -[10:34:31] WARNING: no name column found on line 104 -[10:34:31] WARNING: no name column found on line 105 -[10:34:31] WARNING: no name column found on line 106 -[10:34:31] WARNING: no name column found on line 107 -[10:34:31] WARNING: no name column found on line 108 -[10:34:31] WARNING: no name column found on line 109 -[10:34:31] WARNING: no name column found on line 110 -[10:34:31] WARNING: no name column found on line 111 -[10:34:31] WARNING: no name column found on line 112 -[10:34:31] WARNING: no name column found on line 113 -[10:34:31] WARNING: no name column found on line 114 -[10:34:31] WARNING: no name column found on line 115 -[10:34:31] WARNING: no name column found on line 116 -[10:34:31] WARNING: no name column found on line 117 -[10:34:31] WARNING: no name column found on line 118 -[10:34:31] WARNING: no name column found on line 119 -[10:34:31] WARNING: no name column found on line 120 -[10:34:31] WARNING: no name column found on line 121 -[10:34:31] WARNING: no name column found on line 122 -[10:34:31] WARNING: no name column found on line 123 -[10:34:31] WARNING: no name column found on line 124 -[10:34:31] WARNING: no name column found on line 125 -[10:34:31] WARNING: no name column found on line 126 -[10:34:31] WARNING: no name column found on line 127 -[10:34:31] WARNING: no name column found on line 128 -[10:34:31] WARNING: no name column found on line 129 -[10:34:31] WARNING: no name column found on line 130 -[10:34:31] WARNING: no name column found on line 131 -[10:34:31] WARNING: no name column found on line 132 -[10:34:31] WARNING: no name column found on line 133 -[10:34:31] WARNING: no name column found on line 134 -[10:34:31] WARNING: no name column found on line 135 -[10:34:31] WARNING: no name column found on line 136 -[10:34:31] WARNING: no name column found on line 137 -[10:34:31] WARNING: no name column found on line 138 -[10:34:31] WARNING: no name column found on line 139 -[10:34:31] WARNING: no name column found on line 140 -[10:34:31] WARNING: no name column found on line 141 -[10:34:31] WARNING: no name column found on line 142 -[10:34:31] WARNING: no name column found on line 143 -[10:34:31] WARNING: no name column found on line 144 -[10:34:31] WARNING: no name column found on line 145 -[10:34:31] WARNING: no name column found on line 146 -[10:34:31] WARNING: no name column found on line 147 -[10:34:31] WARNING: no name column found on line 148 -[10:34:31] WARNING: no name column found on line 149 -[10:34:31] WARNING: no name column found on line 150 -[10:34:31] WARNING: no name column found on line 151 -[10:34:31] WARNING: no name column found on line 152 -[10:34:31] WARNING: no name column found on line 153 -[10:34:31] WARNING: no name column found on line 154 -[10:34:31] WARNING: no name column found on line 155 -[10:34:31] WARNING: no name column found on line 156 -[10:34:31] WARNING: no name column found on line 157 -[10:34:31] WARNING: no name column found on line 158 -[10:34:31] WARNING: no name column found on line 159 -[10:34:31] WARNING: no name column found on line 160 -[10:34:31] WARNING: no name column found on line 161 -[10:34:31] WARNING: no name column found on line 162 -[10:34:31] WARNING: no name column found on line 163 -[10:34:31] WARNING: no name column found on line 164 -[10:34:31] WARNING: no name column found on line 165 -[10:34:31] WARNING: no name column found on line 166 -[10:34:31] WARNING: no name column found on line 167 -[10:34:31] WARNING: no name column found on line 168 -[10:34:31] WARNING: no name column found on line 169 -[10:34:31] WARNING: no name column found on line 170 -[10:34:31] WARNING: no name column found on line 171 -[10:34:31] WARNING: no name column found on line 172 -[10:34:31] WARNING: no name column found on line 173 -[10:34:31] WARNING: no name column found on line 174 -[10:34:31] WARNING: no name column found on line 175 -[10:34:31] WARNING: no name column found on line 176 -[10:34:31] WARNING: no name column found on line 177 -[10:34:31] WARNING: no name column found on line 178 -[10:34:31] WARNING: no name column found on line 179 -[10:34:31] WARNING: no name column found on line 180 -[10:34:31] WARNING: no name column found on line 181 -[10:34:31] WARNING: no name column found on line 182 -[10:34:31] WARNING: no name column found on line 183 -[10:34:31] WARNING: no name column found on line 184 -[10:34:31] WARNING: no name column found on line 185 -[10:34:31] WARNING: no name column found on line 186 -[10:34:31] WARNING: no name column found on line 187 -[10:34:31] WARNING: no name column found on line 188 -[10:34:31] WARNING: no name column found on line 189 -[10:34:31] WARNING: no name column found on line 190 -[10:34:31] WARNING: no name column found on line 191 -[10:34:31] WARNING: no name column found on line 192 -[10:34:31] WARNING: no name column found on line 193 -[10:34:31] WARNING: no name column found on line 194 -[10:34:31] WARNING: no name column found on line 195 -[10:34:31] WARNING: no name column found on line 196 -[10:34:31] WARNING: no name column found on line 197 -[10:34:31] WARNING: no name column found on line 198 -[10:34:31] WARNING: no name column found on line 199 -[10:34:31] WARNING: no name column found on line 200 -[10:34:31] WARNING: no name column found on line 201 -[10:34:31] WARNING: no name column found on line 202 -[10:34:31] WARNING: no name column found on line 203 -[10:34:31] WARNING: no name column found on line 204 -[10:34:31] WARNING: no name column found on line 205 -[10:34:31] WARNING: no name column found on line 206 -[10:34:31] WARNING: no name column found on line 207 -[10:34:31] WARNING: no name column found on line 208 -[10:34:31] WARNING: no name column found on line 209 -[10:34:31] WARNING: no name column found on line 210 -[10:34:31] WARNING: no name 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column found on line 198 +[18:49:04] WARNING: no name column found on line 199 +[18:49:04] WARNING: no name column found on line 200 +[18:49:04] WARNING: no name column found on line 201 +[18:49:04] WARNING: no name column found on line 202 +[18:49:04] WARNING: no name column found on line 203 +[18:49:04] WARNING: no name column found on line 204 +[18:49:04] WARNING: no name column found on line 205 +[18:49:04] WARNING: no name column found on line 206 +[18:49:04] WARNING: no name column found on line 207 +[18:49:04] WARNING: no name column found on line 208 +[18:49:04] WARNING: no name column found on line 209 +[18:49:04] WARNING: no name column found on line 210 +[18:49:04] WARNING: no name column found on line 211 +[18:49:04] WARNING: no name column found on line 212 +[18:49:04] WARNING: no name column found on line 213 +[18:49:04] WARNING: no name column found on line 214 +[18:49:04] WARNING: no name column found on line 215 +[18:49:04] WARNING: no name column found on line 216 ...... ---------------------------------------------------------------------- -Ran 10 tests in 0.308s +Ran 10 tests in 0.967s OK .................. ---------------------------------------------------------------------- -Ran 18 tests in 2.079s +Ran 18 tests in 8.659s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.213s +Ran 3 tests in 1.090s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.078s +Ran 8 tests in 0.465s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.050s +Ran 2 tests in 0.247s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.039s +Ran 2 tests in 0.205s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.254s +Ran 1 test in 0.981s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.004s +Ran 8 tests in 0.016s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.009s +Ran 3 tests in 0.052s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.004s +Ran 3 tests in 0.021s OK ...E @@ -42270,28 +42307,28 @@ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- -Ran 4 tests in 0.013s +Ran 4 tests in 0.056s FAILED (errors=1) !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.038s +Ran 7 tests in 0.160s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.042s +Ran 4 tests in 0.205s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 7.814s +Ran 4 tests in 29.337s OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.137s +Ran 10 tests in 0.536s OK . @@ -42301,7 +42338,7 @@ OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.009s +Ran 10 tests in 0.048s OK ....E @@ -42320,15 +42357,15 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 5 tests in 0.104s +Ran 5 tests in 0.350s FAILED (errors=1) !!! TEST FAILURE: python UnitTestGobbi.py {} -................[10:35:14] Molecule does not have explicit Hs. Consider calling AddHs() -[10:35:14] Molecule does not have explicit Hs. Consider calling AddHs() +................[18:51:44] Molecule does not have explicit Hs. Consider calling AddHs() +[18:51:44] Molecule does not have explicit Hs. Consider calling AddHs() ..... ---------------------------------------------------------------------- -Ran 21 tests in 17.441s +Ran 21 tests in 51.504s OK mol_197 @@ -42339,10 +42376,10 @@ 216.26,5.67,105.00,0.87,103.81,0.89,89.27,0.92,6.00 . ---------------------------------------------------------------------- -Ran 1 test in 0.001s +Ran 1 test in 0.009s OK -...[10:35:16] +...[18:51:48] **** Pre-condition Violation @@ -42353,65 +42390,65 @@ . ---------------------------------------------------------------------- -Ran 4 tests in 0.052s +Ran 4 tests in 0.151s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 26.298s +Ran 2 tests in 87.565s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.251s +Ran 2 tests in 1.094s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.028s +Ran 3 tests in 0.093s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.056s +Ran 4 tests in 0.235s OK -.....[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors -[10:35:47] WARNING: not removing hydrogen atom without neighbors +.....[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors +[18:53:35] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- -Ran 10 tests in 0.822s +Ran 10 tests in 3.506s OK -ssssss[10:35:49] No suitable metadata found. -.[10:35:49] No suitable metadata found. +ssssss[18:53:43] No suitable metadata found. +.[18:53:43] No suitable metadata found. ......s/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually warnings.warn( ..... ---------------------------------------------------------------------- -Ran 19 tests in 0.928s +Ran 19 tests in 4.288s OK (skipped=7) sss. ---------------------------------------------------------------------- -Ran 4 tests in 1.640s +Ran 4 tests in 6.871s OK (skipped=3) sss @@ -42421,33 +42458,33 @@ OK (skipped=3) .......... ---------------------------------------------------------------------- -Ran 10 tests in 1.653s +Ran 10 tests in 6.605s OK -..[10:35:56] SMARTS Parse Error: syntax error while parsing: boromicacid -[10:35:56] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -[10:35:56] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -[10:35:56] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -[10:35:56] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -[10:35:56] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -[10:35:56] reaction has no reactants -[10:35:56] reaction has no products -[10:35:56] initialization failed -[10:35:56] reaction has no reactants -[10:35:56] reaction has no products +..[18:54:14] SMARTS Parse Error: syntax error while parsing: boromicacid +[18:54:14] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +[18:54:14] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +[18:54:14] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +[18:54:14] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +[18:54:14] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +[18:54:14] reaction has no reactants +[18:54:14] reaction has no products +[18:54:14] initialization failed +[18:54:14] reaction has no reactants +[18:54:14] reaction has no products . ---------------------------------------------------------------------- -Ran 3 tests in 0.069s +Ran 3 tests in 0.285s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.028s +Ran 4 tests in 0.119s OK .................... ---------------------------------------------------------------------- -Ran 20 tests in 0.299s +Ran 20 tests in 1.251s OK !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} @@ -42461,7 +42498,7 @@ 98% tests passed, 5 tests failed out of 208 -Total Test time (real) = 969.31 sec +Total Test time (real) = 2169.94 sec The following tests FAILED: 22 - pyAlignment (Failed) @@ -42472,7 +42509,7 @@ Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' -dh_auto_test: error: cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 returned exit code 2 +dh_auto_test: error: cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4 returned exit code 2 make[1]: [debian/rules:131: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' create-stamp debian/debhelper-build-stamp @@ -42482,7 +42519,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_auto_install - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/rdkit-202209.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/reproducible-path/rdkit-202209.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/rdkit-202209.3 -B/build/reproducible-path/rdkit-202209.3/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -42493,1382 +42530,1382 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDRandom.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbModule.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbReport.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/StorageUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbResultSet.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbConnection.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbInfo.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Geometry -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Geometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Avalon/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/LazySignature.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/TopNContainer.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitEnsemble.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitEnsembleDb.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/VectCollection.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/HierarchyVis.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Node.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Filter.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Supply.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Output.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesOutput.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbMolSupply.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/demo.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsRemover.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDLogger.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DistanceGeometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/six.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pagesizes.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pidtest.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.ps +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pstests.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pidtest.cpython-311.pyc +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pstests.cpython-311.pyc +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1.1.diff +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/stringformat.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/README -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/pidTK.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/TK/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/utils.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/pidWxDc.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/pidWX.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pidPDF.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfdoc.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgeom.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfutils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgen.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfmetrics.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/psmetrics.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/latin1MetricsCache.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/psmetrics.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/pidPS.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/fontinfo.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PS/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/formatted-strings.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-12.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/metrics.dat +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pilfonts/times-8.pil -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PIL/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pidtest.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/pstests.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/testallps.ps --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pstests.cpython-311.pyc --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/tests/__pycache__/pidtest.cpython-311.pyc --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1.1.diff --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pidPDF.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgen.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfgeom.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfmetrics.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/PDF/pdfdoc.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/Fontmapping.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/colors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/pagesizes.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt4.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Qt/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/ReportLab/pidReportLab.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/colors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/pidPyart.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/Fontmapping.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/sping/Pyart/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitEnsemble.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/TopNContainer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/HierarchyVis.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/LazySignature.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitEnsembleDb.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/VectCollection.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataStructs/BitUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/SimilarityPickers.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/TestRunner.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ScreenComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/BuildComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/AnalyzeComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/BayesComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/Composite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/AdjustComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/GrowComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/NetNode.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/ActFuncs.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/Trainers.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/architecture.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/Network.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/EnrichPlot.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Transforms.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Quantize.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Stats.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/SplitData.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/DataUtils.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/FindQuantBounds.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/MLData.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Quantize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/Transforms.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/CompositeRun.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/Parser.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/CompoundDescriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/VoteImg.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Clusters.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Resemblance.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Standardize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Butina.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/murtagh_test.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/ClusterVis.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Murtagh.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/DataUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Data/SplitData.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitClusterer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitRank.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/entropy.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/files.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/AnalyzeComposite.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/Scoring.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Scoring/Scoring.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/PackageUtils.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/Packager.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ModelPackage/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Tree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/ID3.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/PruneTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeVis.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/randomtest.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildSigTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/DecTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/QuantTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildQuantTree.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Forest.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/SigTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MLUtils/VoteImg.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/CrossValidate.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/ClassificationModel.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/NaiveBayes/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/Risk.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MatOps.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/GrowComposite.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/Network.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/NetNode.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/Trainers.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/ActFuncs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/architecture.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Neural/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/EnrichPlot.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Resemblance.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/murtagh_test.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Standardize.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Murtagh.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/ClusterUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/ClusterVis.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Butina.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/Clusters.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Cluster/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNClassificationModel.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNRegressionModel.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/DistFunctions.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/CrossValidate.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNModel.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/KNNClassificationModel.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/InfoTheory/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/six.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/KNN/DistFunctions.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/CompositeRun.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/AdjustComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/Composite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/BayesComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Composite/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/MoleculeDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/CompoundDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/Descriptors/Parser.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/BuildComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/MatOps.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/Risk.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/SLT/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/QuantTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildSigTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Tree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/PruneTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/Forest.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/SigTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/TreeVis.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/DecTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/BuildQuantTree.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/ID3.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/DecTree/randomtest.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/ML/ScreenComposite.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Numerics/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDLogger.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDConfig.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbModule.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbResultSet.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/StorageUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbInfo.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbReport.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/DbConnection.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Dbase/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SaltRemover.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/BuildFragmentCatalog.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FunctionalGroups.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/ScaffoldNetwork.ipynb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Scaffolds/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/RegistrationHash.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolCatalog.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/BuilderUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeObjects.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeBuilder.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeAligner.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/testCombined.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/standardize.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/tautomer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/resonance.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/normalize.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/errors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/charge.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/test_standardizer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/metal.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/validations.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/fragment.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/validate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/GraphDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapParser.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMaps.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FragmentCatalog.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemicalForceFields.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/TemplateExpand.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/SDFToCSV.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/AlignDepict.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/BulkTester.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors3D.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_orig.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_sa.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/FingerprintUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/Enumerator.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Utils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Torsions.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Sheridan.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Pairs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EnumerateStereoisomers.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ShowMols.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasPatcher.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/aggCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/mplCanvas.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/IPythonConsole.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/cairoCanvas.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/similarityMap1_out2.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/similarityMap1_out.svg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/SimilarityMaps.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/MolDrawing.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/InteractiveRenderer.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/FreeSans.ttf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/canvasbase.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/spingCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/SimilarityMaps.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/qtCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/canvasbase.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/cairoCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/similarityMap1_out.svg -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/MolDrawing.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/mplCanvas.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/InteractiveRenderer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/spingCanvas.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FragmentCatalog.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Draw/aggCanvas.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/inchi.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/github4823.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/Pharmacophore.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/EmbedLib.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/MolSupplier.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/DbMolSupplier.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/DbMolSupplier.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Suppliers/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AllChem.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Crippen.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TorsionFingerprints.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Lipinski.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolSurf.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/BRICS.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Descriptors3D.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ShowMols.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MACCSkeys.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/FraggleSim.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fraggle/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Graphs.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ReducedGraphs.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Torsions.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Pairs.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AtomPairs/Sheridan.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FilterCatalog.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/validate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/tautomer.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/errors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/test_standardizer.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/charge.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/normalize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/fragment.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/standardize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/resonance.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/validations.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/metal.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolStandardize/utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TorsionFingerprints.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MCS.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PandasPatcher.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Randomize.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/BuilderUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeBuilder.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeObjects.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/SubshapeAligner.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Subshape/testCombined.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/fmcs.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/fmcs -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/fmcs/fmcs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/Fingerprinter.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/EState.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/EState_VSA.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/AtomTypes.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FragmentMatcher.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MACCSkeys.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/github4823.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/BRICS.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Recap.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fragments.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TemplateAlign.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/BuildFragmentCatalog.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Randomize.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Generate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/LazyGenerator.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Utils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Matcher.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/SigFactory.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ReducedGraphs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatFinderCLI.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/inchi.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FunctionalGroups.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Graphs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Lipinski.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/AllChem.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PyMol.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolSurf.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_sa.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/FingerprintUtils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolDb/Loader_orig.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EnumerateStereoisomers.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SaltRemover.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FastSDMolSupplier.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/MolKey.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/InchiInfo.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/ShowFeats.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/FeatDirUtilsRD.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SATIS.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/MolKey/InchiInfo.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/ClusterMols.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/FingerprintMols.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/SimilarityScreener.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/MolSimilarity.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/DbFpSupplier.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/FingerprintMols.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FastSDMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/GraphDescriptors.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/MolSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fingerprints/ClusterMols.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/QED.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/Pharmacophore.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/EmbedLib.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/TemplateAlign.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Fragments.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/Enumerator.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SimpleEnum/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/PropertyMol.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMaps.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapParser.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/FeatMapPoint.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FeatMaps/__pycache__ --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/TestRunner.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/BulkTester.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/SDFToCSV.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/AlignDepict.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/ChemUtils/TemplateExpand.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Utils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/SigFactory.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Generate.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/LazyGenerator.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Pharm2D/Matcher.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/FragmentMatcher.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Recap.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/RegistrationHash.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/ShowFeats.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Features/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/Crippen.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/SATIS.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/EState_VSA.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/AtomTypes.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/Chem/EState/EState.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/RDRandom.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbMolSupply.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SDSupply.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/demo.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsRemover.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesSupply.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmilesOutput.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Transform.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Output.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Node.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/Filter.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/VLib/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/Metric/__init__.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/DataManip/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/cactvs.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/listutils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemutils.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/spiral.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/retest.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemdraw_qax.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemdraw.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/cactvs.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/comhack.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/retest.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemutils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/chemdraw.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/spiral.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/fileutils.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/SimilarityPickers.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__init__.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/SimDivFilters/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/python3/dist-packages/rdkit/utils/listutils.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Salts.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/RDData.sqlt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/rddata.sql +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Crippen.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Crippen.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Salts.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Data/RDData.sqlt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/RD.css --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/CodingStandards.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/SGroups.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/CIPLabeling.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Makefile +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example17.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example11.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example10.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example13.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example8.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example2.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example16.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example4.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example9.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example14.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example15.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example6.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example12.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example1.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example5.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example7.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example3.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/RDKit_Book.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Install.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/conf.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/exts +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/exts/extapi.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInC++.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInPython.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp4.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_4.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im0.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png +-- Installing: 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/build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/exts --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/exts/extapi.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example12.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example9.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example3.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example7.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/FindMyRDKit.cmake --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example13.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example8.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example15.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example17.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example5.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example6.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example1.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example14.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example2.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example4.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example16.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example10.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/C++Examples/example11.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/conf.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/BackwardsIncompatibleChanges.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/source/rdkit.Chem.FeatMaps.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book/Install.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png --- Installing: 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--- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png +-- Installing: 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-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/SGroups.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/CodingStandards.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/CIPLabeling.md --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png --- Installing: 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/build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Images --- Installing: 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Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Docs/RD.css -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/MolVS +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md --- Installing: 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Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/ChiralDescriptors.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/README -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/pbf.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/Makefile +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test_list.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/test_list.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test_list.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/search_mmp_db.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_list.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: 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/build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt --- Installing: 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/build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/TestDbCLI.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf --- Installing: 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/build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Fingerprints.sqlt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Descriptors.sqlt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/loadErrors.txt -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/AtomPairs.sqlt --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr/Compounds.sqlt +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/TestDbCLI.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/test.sh -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/README.md +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/test.sh -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/README -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/share/RDKit/license.txt @@ -43911,10 +43948,10 @@ -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/test.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/ConcurrentQueue.h -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail --- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp +-- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp -- Installing: /build/reproducible-path/rdkit-202209.3/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2022.09.3 @@ -44466,15 +44503,15 @@ make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_python3 -ppython3-rdkit I: dh_python3 fs:483: renaming rdBase.so to rdBase.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:483: renaming rdAlignment.so to rdAlignment.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:483: renaming rdForceField.so to rdForceField.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:483: renaming DistGeom.so to DistGeom.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming rdGeometry.so to rdGeometry.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:483: renaming DistGeom.so to DistGeom.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming cDataStructs.so to cDataStructs.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:483: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:483: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:483: renaming rdForceField.so to rdForceField.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming cQuantize.so to cQuantize.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:483: renaming Clustering.so to Clustering.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming rdInfoTheory.so to rdInfoTheory.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:483: renaming Clustering.so to Clustering.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:483: renaming rdAlignment.so to rdAlignment.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming rdAbbreviations.so to rdAbbreviations.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming rdChemReactions.so to rdChemReactions.cpython-311-arm-linux-gnueabihf.so @@ -44511,9 +44548,9 @@ I: dh_python3 fs:483: renaming rdqueries.so to rdqueries.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming rdtrajectory.so to rdtrajectory.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:483: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:483: renaming rdMolStandardize.so to rdMolStandardize.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:483: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:483: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:483: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-311-arm-linux-gnueabihf.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202209.3' dh_installsystemduser -O--buildsystem=cmake -O--parallel @@ -45142,86 +45179,86 @@ dh_strip -a -O--buildsystem=cmake -O--parallel dh_makeshlibs -a -O--buildsystem=cmake -O--parallel dh_shlibdeps -a -O--buildsystem=cmake -O--parallel +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRGroupDecomposition.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolTransforms.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDescriptors.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitChemReactions.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitOptimizer.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolAlign.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDepictor.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitForceField.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDBoost.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolInterchange.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitGraphMol.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSmilesParse.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFilterCatalog.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitga.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitPartialCharges.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolEnumerator.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFMCS.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSubstructMatch.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDGeneral.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitCatalogs.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDeprotect.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitGenericGroups.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMMPA.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolStandardize.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFragCatalog.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolCatalog.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFileParsers.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSubstructMatch.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSimDivPickers.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDataStructs.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitO3AAlign.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitAbbreviations.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFingerprints.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMMPA.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSubstructLibrary.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitga.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitGraphMol.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitOptimizer.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitForceFieldHelpers.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitTautomerQuery.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDGeometryLib.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSLNParse.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRGroupDecomposition.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolDraw2D.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitInfoTheory.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitTautomerQuery.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDistGeometry.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitScaffoldNetwork.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitReducedGraphs.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitShapeHelpers.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitGenericGroups.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDataStructs.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitChemReactions.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDescriptors.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFragCatalog.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitForceField.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitAbbreviations.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSmilesParse.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolAlign.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitAlignment.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitCIPLabeler.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolEnumerator.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSimDivPickers.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDGeneral.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitTrajectory.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitForceFieldHelpers.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitSubgraphs.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFilterCatalog.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitScaffoldNetwork.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitChemicalFeatures.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolCatalog.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDistGeometry.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitFMCS.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolStandardize.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDeprotect.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitCIPLabeler.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolDraw2D.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitEigenSolvers.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolInterchange.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolTransforms.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDepictor.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitPartialCharges.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitTrajectory.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitMolHash.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitChemTransforms.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDGeometryLib.so.1.2022.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitDistGeomHelpers.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitRDBoost.so.1.2022.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitO3AAlign.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitShapeHelpers.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitChemTransforms.so.1.2022.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1/usr/lib/libRDKitAlignment.so.1.2022.09.3 found in none of the libraries dh_installdeb -O--buildsystem=cmake -O--parallel dh_gencontrol -O--buildsystem=cmake -O--parallel +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package python3-rdkit: substitution variable ${python3:Versions} used, but is not defined -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${postgresql:Depends} unused, but is defined -dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package python3-rdkit: substitution variable ${python3:Versions} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined dpkg-gencontrol: warning: package python3-rdkit: substitution variable ${python3:Versions} used, but is not defined dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${postgresql:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${postgresql:Depends} unused, but is defined +dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake -O--parallel dh_builddeb -O--buildsystem=cmake -O--parallel -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202209.3-1_armhf.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202209.3-1_armhf.deb'. +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202209.3-1_armhf.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202209.3-1_all.deb'. dpkg-deb: building package 'postgresql-15-rdkit' in '../postgresql-15-rdkit_202209.3-1_armhf.deb'. dpkg-deb: building package 'postgresql-15-rdkit-dbgsym' in '../postgresql-15-rdkit-dbgsym_202209.3-1_armhf.deb'. -dpkg-deb: building package 'librdkit1' in '../librdkit1_202209.3-1_armhf.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202209.3-1_armhf.deb'. +dpkg-deb: building package 'librdkit1' in '../librdkit1_202209.3-1_armhf.deb'. dpkg-deb: building package 'librdkit1-dbgsym' in '../librdkit1-dbgsym_202209.3-1_armhf.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202209.3-1_all.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202209.3-1_armhf.buildinfo @@ -45231,12 +45268,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/29044/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29044/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/23700 and its subdirectories -I: Current time: Tue Feb 6 10:53:39 -12 2024 -I: pbuilder-time-stamp: 1707260019 +I: removing directory /srv/workspace/pbuilder/29044 and its subdirectories +I: Current time: Wed Feb 7 19:16:27 +14 2024 +I: pbuilder-time-stamp: 1707282987