Diff of the two buildlogs: -- --- b1/build.log 2024-01-11 15:10:58.779450377 +0000 +++ b2/build.log 2024-01-11 15:55:57.013680781 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 11 02:18:38 -12 2024 -I: pbuilder-time-stamp: 1704982718 +I: Current time: Thu Feb 13 11:34:05 +14 2025 +I: pbuilder-time-stamp: 1739396045 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/1227684/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1744204/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +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 12 21:34 /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/1744204/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1744204/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-linux-gnu") + 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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d1bdb07454d14f75a56bc40f2423a163' - 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='1227684' - PS1='# ' - PS2='> ' + INVOCATION_ID=9d15babc6f7d4df3923a3ca92efee0a6 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=1744204 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.XdUZuiZq/pbuilderrc_OTDQ --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.XdUZuiZq/b1 --logfile b1/build.log rdkit_202209.3-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.XdUZuiZq/pbuilderrc_7DLj --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.XdUZuiZq/b2 --logfile b2/build.log rdkit_202209.3-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash @@ -133,15 +165,15 @@ -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 12 21:34 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server @@ -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/1227684/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/1744204/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -603,7 +635,7 @@ Get: 331 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 332 http://deb.debian.org/debian bookworm/main amd64 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 333 http://deb.debian.org/debian bookworm/main amd64 texlive-latex-extra all 2022.20230122-4 [19.2 MB] -Fetched 374 MB in 1min 30s (4146 kB/s) +Fetched 374 MB in 7s (51.4 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 ... 18148 files and directories currently installed.) @@ -1666,8 +1698,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jan 11 14:23:17 UTC 2024. -Universal Time is now: Thu Jan 11 14:23:17 UTC 2024. +Local time is now: Wed Feb 12 21:37:02 UTC 2025. +Universal Time is now: Wed Feb 12 21:37:02 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -2021,7 +2053,11 @@ 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/1744204/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/1744204/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 @@ -2163,7 +2199,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_auto_build - cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202209.3 -B/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -2171,102 +2207,102 @@ make[3]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/External/catch /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/External/catch /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend +cd 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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/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/RDGeneral/Invariant.cpp -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202209.3/Code/RDStreams/streams.cpp -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o +[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 1%] Built target catch -[ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -[ 1%] Built target inchi_support +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 0%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o +make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend +make[4]: Leaving directory 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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/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 +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu 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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 -fPIC -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hc.c.o -MF CMakeFiles/hc.dir/hc.c.o.d -o CMakeFiles/hc.dir/hc.c.o -c /build/reproducible-path/rdkit-202209.3/Code/ML/Cluster/Murtagh/hc.c [ 4%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_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/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202209.3/External/GA/util/Util.cpp [ 5%] Linking C shared library ../../../../lib/libRDKithc.so @@ -2298,151 +2334,137 @@ 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-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/DataStructs 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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 -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 +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-x86_64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make 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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/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 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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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/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 -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.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-x86_64-linux-gnu' +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make 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-Wdate-time -D_FORTIFY_SOURCE=2 -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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build +make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build +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-x86_64-linux-gnu' +[ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build -[ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o +[ 6%] Building CXX object 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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/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 -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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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/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 +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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%] Linking CXX executable testMatCalc cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 5%] Built target testMatCalc -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -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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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 6%] Linking CXX executable testConcurrentQueue cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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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/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 +[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 6%] Built target testConcurrentQueue -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 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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/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 +[ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 6%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.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,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so [ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu/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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so [ 6%] Built target EigenSolvers -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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-x86_64-linux-gnu/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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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%] Built target Catalogs -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 7%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 7%] Built target SimDivPickers -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make 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-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, @@ -2460,21 +2482,25 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 8%] Linking CXX executable testMatrices +[ 7%] Linking CXX executable testMatrices cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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-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-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 8%] Built target testQuery -[ 8%] Linking CXX executable testSimDivPickers -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +[ 8%] Built target SimDivPickers +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 8%] Built target testSimDivPickers +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-x86_64-linux-gnu' +[ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 [ 8%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so @@ -2488,20 +2514,20 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build +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-x86_64-linux-gnu' -[ 8%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 8%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 8%] Linking CXX executable testRDValue -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +[ 8%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 8%] Linking CXX executable testQuery +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 8%] Built target testRDValue +[ 8%] Built target testQuery [ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 @@ -2509,8 +2535,8 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 8%] 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-x86_64-linux-gnu' 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= @@ -2518,73 +2544,78 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= +make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= -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-x86_64-linux-gnu' -make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap 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-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/Transform2D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 8%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK 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+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-x86_64-linux-gnu' +make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build [ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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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 -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 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 10%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 10%] Linking CXX executable testDict -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +[ 10%] Linking CXX executable testSimDivPickers +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 +[ 10%] Linking CXX executable testRDValue +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/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 +/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-x86_64-linux-gnu' +[ 10%] Built target testSimDivPickers make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 10%] Built target testDict [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 10%] Built target testRDValue +[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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, @@ -2603,6 +2634,13 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 10%] Linking CXX executable testDict +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 10%] Built target testDict +[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -2617,7 +2655,7 @@ 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/DataStructs/Wrap/DiscreteValueVect.cpp:11: + 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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2638,10 +2676,6 @@ /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/GridUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -2660,6 +2694,8 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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 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, @@ -2678,11 +2714,15 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 10%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 -[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' [ 10%] Built target InfoTheory @@ -2694,26 +2734,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 11%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 11%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so @@ -2727,31 +2747,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 11%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/Data && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 11%] Linking CXX executable testMultiFPB -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 [ 11%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 11%] Built target testMultiFPB -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so -[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 11%] Built target RDGeometryLib -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -2770,6 +2768,11 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 11%] Built target RDGeometryLib +[ 11%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -2784,10 +2787,12 @@ 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/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: + 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%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.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, @@ -2806,24 +2811,50 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 12%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 12%] Built target rdMetricMatrixCalc -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend +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/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( + | ^~~~~~~~~~~~~~~~~~~~ +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build +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-x86_64-linux-gnu' +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 executable testFPB cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 /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-x86_64-linux-gnu' [ 12%] Built target testFPB +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= @@ -2846,7 +2877,7 @@ 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/HierarchicalClusterPicker.cpp:13: + 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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2860,32 +2891,13 @@ 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/Data/cQuantize.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.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%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 12%] Built target cQuantize -make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 13%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/testGrid.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, @@ -2896,13 +2908,33 @@ 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/DataStructs/Wrap/wrap_SparseBV.cpp:11: + 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/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 12%] Linking CXX executable testMultiFPB +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 12%] Built target testMultiFPB +make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 13%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/Geometry/testGrid.cpp +[ 13%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../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, @@ -2910,24 +2942,19 @@ 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_ExplicitBV.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/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/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 13%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -/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-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 13%] Built target Alignment +[ 13%] Built target rdSimDivPickers 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= @@ -2936,6 +2963,26 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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 +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +[ 13%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 13%] Built target Alignment +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 13%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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, @@ -2946,39 +2993,53 @@ 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/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: + 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( | ^~~~~~~~~~~~~~~~~~~~ +[ 13%] Built target cQuantize /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-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 14%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.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/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../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-x86_64-linux-gnu' -[ 14%] Built target rdSimDivPickers 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 14%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o +[ 13%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 14%] Built target testTransforms 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 14%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o +[ 13%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 13%] Linking CXX executable testGrid +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 13%] Built target testGrid +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 13%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 13%] Built target ChemicalFeatures +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 13%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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, @@ -2986,22 +3047,19 @@ 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/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/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 14%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 14%] Linking CXX executable testTransforms +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.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/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.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, @@ -3021,15 +3079,25 @@ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 14%] Built target testDataStructs -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= +[ 14%] Built target testTransforms +[ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 14%] Linking CXX executable testDataStructs +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 14%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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%] Built target testDataStructs +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 14%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../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, @@ -3040,35 +3108,17 @@ 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: + 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 14%] Linking CXX executable testGrid -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 -[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 14%] Built target testGrid -[ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 14%] Built target rdInfoTheory [ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 14%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 14%] Built target rdInfoTheory -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3108,25 +3158,16 @@ [ 15%] Linking CXX executable testAlignment cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 -[ 15%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 15%] Built target testAlignment [ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 15%] Built target ChemicalFeatures -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= +[ 15%] Linking CXX executable testChemicalFeatures +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +[ 15%] Built target testChemicalFeatures [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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, @@ -3146,10 +3187,32 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 16%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 16%] Built target rdAlignment +[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +/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) { + | ~~~~~~~~~~~~~^~~ [ 16%] Linking CXX static library librdkitCatch.a cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 16%] Built target rdkitCatch +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 16%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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/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, @@ -3160,7 +3223,7 @@ 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 /build/reproducible-path/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3177,53 +3240,17 @@ 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: + 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -/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) { - | ~~~~~~~~~~~~~^~~ -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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'/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 16%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 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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 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 16%] Linking CXX executable testChemicalFeatures -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 16%] Built target testChemicalFeatures -make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake 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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/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/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, @@ -3234,92 +3261,74 @@ 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_Utils.cpp:11: + 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( | ^~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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/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 -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED 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Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral/CMakeFiles/logTestsCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 16%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 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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/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 +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD 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-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/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 make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E 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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/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 -[ 16%] Linking CXX executable logTestsCatch +[ 17%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 16%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o +[ 17%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 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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/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 -[ 17%] Linking CXX executable dictTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 17%] Built target dictTestsCatch +[ 17%] Built target logTestsCatch [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AddHs.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 17%] Linking CXX executable testConrec -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 17%] Built target testConrec -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.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/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 18%] Built target cDataStructs -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp: In instantiation of 'static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = int; std::istream = std::basic_istream]': /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 = int; std::istream = std::basic_istream]' /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:854:27: required from here @@ -3330,17 +3339,44 @@ /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:1666:37: warning: comparison is always false due to limited range of data type [-Wtype-limits] -[ 18%] Linking CXX executable pickersTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 18%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.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/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 18%] Built target pickersTestsCatch +[ 18%] Built target cDataStructs +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/AddHs.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Linking CXX executable testConrec +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 18%] Built target testConrec +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Resonance.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Resonance.cpp +[ 19%] Linking CXX executable geometryTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +[ 19%] Linking CXX executable pickersTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 19%] Built target pickersTestsCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Built target geometryTestsCatch +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Resonance.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/StereoGroup.cpp.o -MF CMakeFiles/GraphMol.dir/StereoGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/StereoGroup.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o @@ -3349,6 +3385,15 @@ cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 20%] Built target rdBase 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, @@ -3364,15 +3409,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 module ../../../rdkit/rdBase.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 20%] Built target rdBase [ 20%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -3381,224 +3417,178 @@ [ 20%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend -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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= make -f 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'/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler 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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/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/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make 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-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 +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -[ 21%] 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Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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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/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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build -cd 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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/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 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 21%] Building CXX object 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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 -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 +[ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o +[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o [ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ 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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/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 -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_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 -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/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= +[ 22%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 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-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 -[ 22%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 22%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so +[ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 22%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/libRDKitPartialCharges.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.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,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/x86_64-linux-gnu/libboost_serialization.so +[ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2022.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 22%] Built target MolCatalog -make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.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-x86_64-linux-gnu' -[ 22%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 22%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so +[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 22%] Built target GenericGroups +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 23%] Built target MolCatalog 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 22%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o +[ 23%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 23%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.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,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/x86_64-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 23%] Built target PartialCharges -[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -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/rdqueries.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 -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= +[ 23%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 24%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 23%] Built target Trajectory 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o +[ 23%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 24%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +[ 23%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 23%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 24%] Built target MolTransforms +[ 23%] Built target Subgraphs 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 24%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o +[ 23%] Building CXX object Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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/Trajectory.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( - | ^~~~~~~~~~~~~~~~~~~~ +[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 23%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 23%] Built target GenericGroups +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 23%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -3616,14 +3606,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 25%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -3631,42 +3613,19 @@ 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/GraphMol/Wrap/rdTrajectory.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/GraphMol/Wrap/rdqueries.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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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-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 -[ 25%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 25%] Built target Subgraphs -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 25%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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, @@ -3681,10 +3640,32 @@ 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/PartialCharges/Wrap/rdPartialCharges.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.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( | ^~~~~~~~~~~~~~~~~~~~ +[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 23%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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, @@ -3699,26 +3680,26 @@ 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/Queries.cpp:11: + 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( | ^~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 25%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' [ 25%] Built target Optimizer -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build +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-x86_64-linux-gnu' -[ 25%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -3726,21 +3707,17 @@ 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/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/ChemicalFeatures/Wrap/FreeChemicalFeature.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/GraphMol/MolCatalog/Wrap/rdMolCatalog.h:15, + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp:5: /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +/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, @@ -3755,29 +3732,23 @@ 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/MolTransforms/Wrap/rdMolTransforms.cpp:12: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Queries.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( | ^~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 26%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so [ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 26%] Built target SmilesParse +[ 26%] Built target rdPartialCharges 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake --color= +[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 26%] Built target rdPartialCharges [ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend @@ -3788,21 +3759,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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26%] Built target rdtrajectory -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 26%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 26%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -3810,57 +3766,82 @@ 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/MolCatalog/Wrap/rdMolCatalog.h:15, - from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp:5: + 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/Trajectory.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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 26%] Linking CXX executable testOptimizer -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 26%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o +cd 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/usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 26%] Built target testOptimizer -make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend +[ 26%] Built target rdChemicalFeatures +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 27%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -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/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 +[ 27%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 27%] Built target rdChemicalFeatures -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend +[ 27%] Built target SmilesParse +make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build +make -f 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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/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 +[ 27%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 27%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 In file included from /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.h:17, from /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:11: In copy constructor 'RDKit::Snapshot::Snapshot(const RDKit::Snapshot&)', @@ -3876,20 +3857,21 @@ /build/reproducible-path/rdkit-202209.3/Code/ForceField/ForceField.cpp:281:10: note: 'finalForce' was declared here 281 | double finalForce; | ^~~~~~~~~~ -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -cd 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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 -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 28%] Built target testOptimizer +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build +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-x86_64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Nonbonded.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, @@ -3897,149 +3879,181 @@ 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/Substruct/SubstructUtils.cpp:13: + 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( | ^~~~~~~~~~~~~~~~~~~~ -[ 28%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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-DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 28%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 28%] Built target SLNParse +[ 28%] Built target rdMolCatalog +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 28%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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-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 +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Inversion.cpp +[ 29%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/TorsionAngle.cpp +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 29%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 29%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 29%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 29%] Built target graphmolcpTest +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o +[ 29%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 28%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 28%] Linking CXX executable graphmolcpTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so +[ 29%] Linking CXX executable graphmolIterTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 28%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -[ 28%] Built target ShapeHelpers +[ 29%] Built target graphmolIterTest 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 29%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ 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/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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/catch_tests.cpp -[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -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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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 28%] Building CXX object 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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 -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 29%] Linking CXX executable graphmolMemTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +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/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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 [ 29%] Linking CXX executable test-valgrind cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 29%] Built target test-valgrind -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= -[ 29%] Built target graphmolMemTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake --color= +[ 29%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -[ 29%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so +make -f 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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/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 -[ 29%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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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 -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2022.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.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/x86_64-linux-gnu/libboost_serialization.so -[ 29%] Linking CXX executable smiTest2 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/PositionConstraint.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 29%] Built target smiTest2 +[ 29%] Built target ShapeHelpers 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake --color= -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD 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-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 +[ 30%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 30%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Params.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/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 29%] Built target graphmolIterTest -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Inversion.cpp -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 31%] Built target rdtrajectory +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' 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, @@ -4047,52 +4061,46 @@ 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: + 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/Substruct/SubstructUtils.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( | ^~~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 29%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +[ 31%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 31%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 29%] Built target SubstructMatch -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -cd 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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/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 -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION 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-c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp +[ 32%] Built target testPartialCharges +[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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, @@ -4125,215 +4133,227 @@ 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/SLNParse/Wrap/rdSLNParse.cpp:35: + 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( | ^~~~~~~~~~~~~~~~~~~~ -[ 31%] Linking CXX executable testSubgraphs2 +[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistanceConstraint.cpp.o -MF 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 +[ 32%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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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/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleConstraint.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1 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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 -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 +[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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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/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 +[ 34%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 library ../../../lib/libRDKitSLNParse.so +cd 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../../../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/x86_64-linux-gnu/libboost_serialization.so +/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 34%] Built target SLNParse +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake --color= +[ 34%] Built target SubstructMatch +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 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Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o +[ 34%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 -[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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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-I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -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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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/querytest.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 -[ 32%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 32%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so -[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/UFF/Params.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 33%] Built target rdSLNParse +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/CIPLabeler/Wrap/rdCIPLabeler.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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 33%] Built target CIPLabeler 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= +[ 35%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o +[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/AngleBend.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 33%] Built target rdMolInterchange 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o +[ 35%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 33%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +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/SLNParse/Wrap/rdSLNParse.cpp:35: +/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( + | ^~~~~~~~~~~~~~~~~~~~ +[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +[ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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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/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 -[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD 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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/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 shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && 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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/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 -[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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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 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 36%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 36%] Built target graphmolqueryTest -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= +[ 36%] Built target ForceField make -f 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directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 36%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK 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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/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 -[ 36%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/DistanceConstraint.cpp.o -MF 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 +[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ 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CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp +[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 executable moliteratorTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/moliteratorTestsCatch.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/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 36%] Built target moliteratorTestsCatch 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake --color= @@ -4342,120 +4362,118 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 36%] Building CXX object 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/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/CIPLabeler/Wrap/rdCIPLabeler.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. 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+cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 38%] Built target ChemTransforms +[ 36%] Built target MolAlign 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor 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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/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%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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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/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%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g 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-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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 39%] Built target ReducedGraphs -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend +[ 38%] Built target graphmolqueryTest +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake 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'/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build +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-x86_64-linux-gnu' -[ 39%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 39%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2022.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +[ 38%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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/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 +[ 38%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS 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Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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-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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 39%] Built target MolChemicalFeatures -make -f 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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/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 -[ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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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/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 +[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.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, @@ -4474,10 +4492,36 @@ /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/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp +[ 41%] Linking CXX executable testReducedGraphs +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 42%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -4485,34 +4529,87 @@ 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/Wrap/rdchem.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/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( | ^~~~~~~~~~~~~~~~~~~~ -/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/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 41%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 41%] Built target ForceField -[ 41%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 41%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so +[ 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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 42%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 42%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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smaTest1 +[ 42%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -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/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 42%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 42%] Built target MolChemicalFeatures +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 42%] Linking CXX executable testSLNParse +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.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, @@ -4523,21 +4620,29 @@ 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: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/rdchem.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%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 /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/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -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/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -cd 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-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 -[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 42%] Built target testSLNParse +[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 42%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 42%] Built target FilterCatalog +[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 42%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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, @@ -4552,10 +4657,18 @@ 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/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.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( | ^~~~~~~~~~~~~~~~~~~~ +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 42%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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, @@ -4570,39 +4683,14 @@ 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: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/Table.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%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 42%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 42%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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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/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%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -4610,49 +4698,16 @@ 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/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.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/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 43%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 43%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -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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"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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 43%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /usr/bin/c++ 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CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -[ 43%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 43%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 43%] Built target rdMolChemicalFeatures -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +/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, @@ -4667,68 +4722,28 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ -[ 43%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/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 -[ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 44%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 44%] Built target FilterCatalog -[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2022.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so +[ 43%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 +[ 43%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 44%] Built target FragCatalog -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +[ 43%] Built target Depictor +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build +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-x86_64-linux-gnu' -[ 44%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 44%] Linking CXX executable testReducedGraphs -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 44%] Built target testReducedGraphs -[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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/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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 45%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 43%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.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, @@ -4747,13 +4762,16 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 45%] Built target Fingerprints -[ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 45%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 43%] 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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 43%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -4768,17 +4786,30 @@ 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/Wrap/Table.cpp:13: + 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( | ^~~~~~~~~~~~~~~~~~~~ -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 44%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 45%] Built target rdReducedGraphs -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 44%] Built target FragCatalog +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 45%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 46%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -4797,10 +4828,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -4815,18 +4842,10 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 47%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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, @@ -4845,6 +4864,10 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 46%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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, @@ -4859,13 +4882,20 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 47%] Linking CXX shared library ../../../lib/libRDKitDepictor.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 +[ 46%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 46%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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, @@ -4880,27 +4910,10 @@ 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/Wrap/RingInfo.cpp:12: + 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( | ^~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 47%] Built target Depictor -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 47%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -4915,10 +4928,25 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ +[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 47%] Built target rdAbbreviations +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 47%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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, @@ -4933,10 +4961,29 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ +[ 47%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 47%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 47%] Built target rdMolChemicalFeatures +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 48%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -4950,17 +4997,29 @@ 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: + 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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 47%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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../../../../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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 48%] Built target rdDepictor +[ 48%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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-DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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/EditableMol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 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, @@ -4974,17 +5033,11 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ -/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 module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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, @@ -4998,22 +5051,31 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 48%] Built target rdAbbreviations -make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 50%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +[ 50%] Built target O3AAlign +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 50%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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, @@ -5027,27 +5089,21 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ -/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/libRDKitForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 48%] 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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= +[ 50%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 50%] Built target Fingerprints +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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, @@ -5066,16 +5122,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -5089,7 +5135,7 @@ 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/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -5109,15 +5155,15 @@ 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: + 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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, @@ -5131,11 +5177,37 @@ 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: + 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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 50%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 50%] Built target DistGeometry +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 50%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 50%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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, @@ -5150,20 +5222,10 @@ 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/Depictor/Wrap/rdDepictor.cpp:11: + 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( | ^~~~~~~~~~~~~~~~~~~~ -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 48%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 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, @@ -5177,56 +5239,40 @@ 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/ForceFieldHelpers/Wrap/rdForceFields.cpp: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( | ^~~~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o +/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-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 -[ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 49%] Built target rdFingerprintGenerator -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 49%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 49%] Built target rdDepictor -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/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/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 -[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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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/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 [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +[ 50%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 50%] Built target rdForceField +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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/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, @@ -5240,67 +5286,60 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 50%] Built target rdForceFieldHelpers -[ 50%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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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 -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 -[ 51%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 51%] Built target O3AAlign -[ 51%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ 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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 -[ 51%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl [ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 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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/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 -[ 51%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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=. 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../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 51%] 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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers 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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/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 +[ 52%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 52%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -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/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileWriter.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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/XYZFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileParser.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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/MaeMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers/SequenceParsers.cpp -[ 52%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 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/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( + | ^~~~~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_64BIT_BUILD -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 +[ 52%] Linking CXX executable testDistGeom +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 52%] Built target rdForceField +[ 52%] Built target testDistGeom make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make 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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/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 [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ 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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 -[ 53%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 53%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 54%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 53%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 53%] Built target rdfiltercatalog -[ 53%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +[ 54%] Built target DistGeomHelpers +[ 54%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 53%] Built target DistGeom -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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 53%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so +[ 54%] Built target DistGeom +[ 54%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.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,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2022.09.3 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.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 ../../../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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1 ../../../lib/libRDKitFileParsers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 53%] Built target FileParsers +[ 54%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= +make -f 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-DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake --color= +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +[ 55%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol 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-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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend 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-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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 54%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake --color= -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make 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'/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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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/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 -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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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 -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/catch_sgroups.cpp -[ 55%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script 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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 [ 56%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 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graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 58%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 58%] Built target graphmoltestPicklerGlobalSetting +[ 58%] Built target hanoiTest 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/DependInfo.cmake --color= @@ -5567,11 +5611,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 -[ 58%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 58%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 58%] Built target testUFFForceField +[ 58%] Built target graphmoltestPicklerGlobalSetting 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/DependInfo.cmake --color= @@ -5580,11 +5624,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/test.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/smiTest1.dir/test.cpp.o -MF CMakeFiles/smiTest1.dir/test.cpp.o.d -o CMakeFiles/smiTest1.dir/test.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SmilesParse/test.cpp -[ 58%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 58%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 58%] Linking CXX executable testUFFForceField +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 58%] Built target hanoiTest +[ 58%] Built target testUFFForceField make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake --color= @@ -5593,9 +5640,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 58%] Linking CXX executable graphmolSGroupCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 58%] Built target graphmolSGroupCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend @@ -5632,15 +5676,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 58%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 58%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so [ 58%] Linking CXX executable testSGroup cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 -[ 58%] Built target canonTestsCatch -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' /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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 58%] Built target testMMFFForceField +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' @@ -5648,11 +5692,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 +[ 59%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 59%] Built target testSGroup 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.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/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' @@ -5661,34 +5708,31 @@ [ 60%] Linking CXX executable graphmolTest1 cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.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/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../lib/libRDKitForceField.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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitSubstructMatch.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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 60%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 60%] Built target graphmolTest1 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 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/build/reproducible-path/rdkit-202209.3 /build/reproducible-path/rdkit-202209.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build +[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 61%] Linking CXX executable testDepictor -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.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/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../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/x86_64-linux-gnu/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/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libz.so +[ 61%] Linking CXX executable depictorCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 61%] Built target testDepictor +[ 61%] Built target depictorCatch 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake --color= @@ -5697,14 +5741,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 61%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 61%] Linking CXX executable nontetrahedralCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 61%] Linking CXX executable cxsmilesTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.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/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 61%] Built target graphmoltestPickler +[ 61%] Built target cxsmilesTest 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= @@ -5713,21 +5754,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 +[ 61%] Linking CXX executable testDepictor +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.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/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../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/x86_64-linux-gnu/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/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 61%] Built target nontetrahedralCatch +[ 61%] Built target testDepictor 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' +[ 61%] Linking CXX executable nontetrahedralCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 61%] Linking CXX executable cxsmilesTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.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/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../../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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 61%] Built target cxsmilesTest +[ 61%] Built target nontetrahedralCatch 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= @@ -5736,63 +5780,63 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 61%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 62%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 62%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.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/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 61%] Built target testGeneralFileReader +[ 62%] Built target graphmoltestChirality 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 61%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 61%] Built target testSequence +[ 62%] Built target testMultithreadedMolSupplier 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 61%] Linking CXX executable testMol2ToMol +[ 62%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 62%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 62%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 62%] Built target testMol2ToMol 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 62%] Built target graphmoltestChirality +[ 62%] Built target testTplParser 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-x86_64-linux-gnu' +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o +[ 62%] Linking CXX executable graphmoltestPickler cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -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 -[ 62%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.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/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 62%] Built target testMultithreadedMolSupplier +[ 62%] Built target graphmoltestPickler 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= @@ -5801,53 +5845,50 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 62%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 62%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 62%] Built target testExtendedStereoParsing +[ 62%] Built target testSequence make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.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/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 62%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build make[4]: Entering directory 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../../../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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so [ 63%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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'/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 63%] Built target testExtendedStereoParsing make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend +[ 63%] Built target testGeneralFileReader make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake --color= -make[4]: Leaving directory 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/usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 63%] Built target graphmolTestsCatch 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 63%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 [ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 63%] Linking CXX executable XYZFileParserCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat 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../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 63%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 63%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 63%] Built target XYZFileParserCatchTest +[ 63%] Built target testMolWriter 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= @@ -5856,8 +5897,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 63%] Linking CXX executable XYZFileParserCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.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/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 63%] Built target chiralityTestsCatch +[ 63%] Built target XYZFileParserCatchTest 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= @@ -5866,11 +5910,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 -[ 63%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 63%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 63%] Built target testMolWriter +[ 63%] Built target graphmolTestsCatch 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= @@ -5879,13 +5923,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 63%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 63%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 63%] Built target substructTestCatch +[ 63%] Built target chiralityTestsCatch make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/DependInfo.cmake --color= @@ -5894,37 +5936,39 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 64%] Linking CXX executable testMolSupplier -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so +[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 64%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 64%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 64%] Built target testMolSupplier +[ 64%] Built target cdxmlParserCatchTest 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 64%] Built target substructTestCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 64%] Linking CXX executable testGenericGroups -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 64%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 64%] Built target testGenericGroups 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= +[ 64%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 64%] Built target cdxmlParserCatchTest +[ 64%] Built target testGenericGroups 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake --color= @@ -5936,36 +5980,55 @@ [ 64%] Linking CXX executable testPropertyLists cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 64%] Linking CXX executable testMolSupplier +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 64%] Built target testPropertyLists -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 65%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 65%] Built target smiTest1 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o +[ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp -[ 65%] Linking CXX executable smiTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 65%] Built target smiTestCatch +[ 64%] Built target testMolSupplier 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o +[ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 65%] Built target testSubstructMatch +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 65%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 65%] Built target smiTest1 +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-x86_64-linux-gnu' +cd 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Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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, @@ -5984,75 +6047,24 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 65%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so [ 65%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o cd 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../../../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/x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 65%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 65%] Built target filterCatalogTest -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 65%] Built target testSubstructMatch -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 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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/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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 65%] Linking CXX executable chemTransformsTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 65%] Linking CXX executable testMHFPFingerprint -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 65%] Built target chemTransformsTestCatch +[ 65%] Built target smiTestCatch 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 65%] Built target testMHFPFingerprint -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= [ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 65%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 65%] Built target testFragCatalog -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 65%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so 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, @@ -6094,6 +6106,55 @@ /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))); | ^ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 65%] Built target filterCatalogTest +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 65%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 65%] Built target testMHFPFingerprint +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +[ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 65%] Linking CXX executable testFragCatalog +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 65%] Linking CXX executable chemTransformsTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake 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Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 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, @@ -6112,176 +6173,127 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 67%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so 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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 -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 -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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%] Linking CXX executable testChemTransforms +[ 65%] Linking CXX executable testChemTransforms cd 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../../../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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 67%] Built target testMolTransforms +[ 65%] Built target testChemTransforms 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o +[ 65%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 68%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 68%] Built target testCrystalForceField -[ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 65%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target testMMFFForceFieldHelpersMultiThread +[ 65%] Built target testMolTransforms 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o +[ 65%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 -[ 68%] Linking CXX executable fpTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 65%] Linking CXX executable testCrystalForceField +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target fpTestCatch +[ 65%] Built target testCrystalForceField 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o +[ 65%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 68%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 68%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.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/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 66%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target testMMFFForceFieldHelpers +[ 66%] Built target testMMFFForceFieldHelpersMultiThread 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o +[ 66%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.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/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 66%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target fileParsersCatchTest +[ 66%] Built target testMMFFForceFieldHelpers 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o +[ 66%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -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/FragCatalog/Wrap/FragCatParams.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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 68%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target graphmolMolOpsTest +[ 66%] Built target fpTestCatch 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o +[ 66%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 68%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 66%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +[ 66%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target testFingerprintGenerators +[ 66%] Built target graphmolMolOpsTest 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o +[ 66%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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/FragCatalog/Wrap/FragCatGenerator.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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/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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--color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 67%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 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Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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../../../../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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target testUFFForceFieldHelpers -make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make 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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 -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/x86_64-linux-gnu/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 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 68%] Linking CXX executable molAlignCatchTest +[ 67%] Linking CXX executable molAlignCatchTest cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -[ 68%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target molAlignCatchTest -make -f 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-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 +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o +cd 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-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 [ 68%] Linking CXX executable testShapeHelpers cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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/usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target testShapeHelpers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 68%] Built target molAlignCatchTest 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-x86_64-linux-gnu' +[ 68%] Built target testShapeHelpers cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 68%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 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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/FragCatalog/Wrap/FragCatParams.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( + | ^~~~~~~~~~~~~~~~~~~~ [ 68%] Linking CXX executable distGeomHelpersCatch cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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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/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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 68%] Built target testUFFForceFieldHelpers +[ 68%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +[ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o +/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 68%] Built target testFeatures +[ 69%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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, @@ -6396,58 +6421,67 @@ 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/FragCatalog/Wrap/FragFPGenerator.cpp:11: + 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( | ^~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 68%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +[ 69%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 70%] Linking CXX executable trajectoryTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 +[ 70%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libz.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 68%] Built target MMPA -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 68%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -[ 68%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target testFingerprints +[ 70%] Built target trajectoryTest +[ 70%] Built target MMPA make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend +[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +[ 70%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -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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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target testFeatures +[ 70%] Built target rdDistGeom 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o +[ 70%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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/usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 68%] Built target rdDistGeom -[ 69%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 70%] Built target molInterchangeCatchTest +[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong 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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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 70%] Built target testFingerprints +[ 70%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 70%] Linking CXX executable molInterchangeTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.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, @@ -6466,6 +6500,10 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 70%] Built target molInterchangeTest1 +[ 70%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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, @@ -6480,30 +6518,35 @@ 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/FragCatalog/Wrap/FragCatGenerator.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( | ^~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 70%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 70%] Built target molInterchangeCatchTest -[ 70%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 71%] Linking CXX executable trajectoryTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so 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/usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 71%] Built target trajectoryTest -[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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target testDistGeomHelpers +[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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, + 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/FragCatalog/Wrap/FragFPGenerator.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, @@ -6524,27 +6567,14 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so 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-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 -[ 71%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E 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-D_FORTIFY_SOURCE=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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 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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/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 +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -6563,28 +6593,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 72%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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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/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%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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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/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 -[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 72%] Built target rdMMPA -[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -6603,9 +6611,44 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 72%] Linking CXX executable testAbbreviations cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 72%] Built target rdfragcatalog +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/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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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 72%] Linking CXX executable testMMPA +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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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/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 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, @@ -6624,22 +6667,12 @@ /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-x86_64-linux-gnu' -[ 72%] Built target testAbbreviations [ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Descriptors/WHIM.cpp [ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat 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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/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 -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -6658,6 +6691,14 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o @@ -6680,28 +6721,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 74%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libz.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/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( - | ^~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.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, @@ -6720,40 +6739,64 @@ /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 shared library ../../../lib/libRDKitFMCS.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libz.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' [ 74%] Built target FMCS make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend -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-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= 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Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 74%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 74%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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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/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 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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/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( + | ^~~~~~~~~~~~~~~~~~~~ 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, @@ -6790,13 +6833,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 74%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 74%] Built target testMMFFForceField -[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -6819,6 +6855,8 @@ cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -6837,27 +6875,30 @@ /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/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 74%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 75%] Linking CXX executable FMCStest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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-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 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../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 75%] Built target FMCStest [ 76%] Linking CXX executable testFMCS cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 76%] Built target testFMCS +[ 76%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 76%] Built target rdFMCS [ 76%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -6866,281 +6907,256 @@ [ 76%] Built target Descriptors make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend 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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake --color= make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend -make -f Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/depend -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-x86_64-linux-gnu' -make -f 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/DependInfo.cmake --color= +make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202209.3 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/usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd 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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 +[ 82%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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 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Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 80%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 81%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -[ 81%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +[ 82%] Built target testO3AAlign +[ 82%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/CDXMLParser.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 82%] Built target rgroupCatchTests -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitga.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 82%] Built target rdRGroupDecomposition -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../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, @@ -7300,129 +7333,120 @@ /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-x86_64-linux-gnu' -[ 82%] Built target rdMolAlign -[ 82%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 82%] Built target testRGroupDecompInternals -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 83%] Built target rdMolHash -[ 83%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 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-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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator 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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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap 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directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build +[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +[ 83%] Building CXX object 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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/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 make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= +[ 83%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +[ 83%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolStandardize/Metal.cpp +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 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../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 84%] Built target molHashCatchTest +[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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, @@ -7460,6 +7484,14 @@ /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 /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/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, @@ -7493,58 +7525,69 @@ /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 /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++); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -[ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +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( + | ^~~~~~~~~~~~~~~~~~~~ [ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 84%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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/usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so [ 85%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 85%] Built target testReactionFingerprints +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' [ 85%] Built target Deprotect +[ 85%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 86%] Built target rdMolDescriptors 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -[ 85%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o +[ 86%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 -[ 85%] Linking CXX executable testReactionFingerprints -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 85%] Built target testReactionFingerprints -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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../../../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/x86_64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 86%] Built target testEnumeration -[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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, @@ -7559,28 +7602,25 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ -[ 87%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so -[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2022.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +[ 86%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 87%] Built target MolEnumerator -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 86%] Built target testEnumeration +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= +cd 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../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 87%] Built target deprotectTest -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend +[ 88%] Built target deprotectTest +[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 88%] Built target MolEnumerator +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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build +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-x86_64-linux-gnu' -[ 87%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK 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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 +[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -7656,38 +7714,8 @@ /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:30: note: '' declared here 129 | ROMOL_SPTR react = python::extract(reactant); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK 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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 -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 -[ 88%] Building CXX object 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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/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 -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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, @@ -7703,46 +7731,35 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 89%] Linking CXX executable rxnTestCatch +cd 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../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/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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../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 88%] Built target rdDeprotect -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 -[ 88%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 88%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 88%] Built target rdMolEnumerator -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 89%] Built target rxnTestCatch +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-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 89%] Built target testMolEnumerator -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +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-x86_64-linux-gnu' +[ 89%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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/TransformCatalog/TransformCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT 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CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMol.cpp [ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 -[ 89%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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, @@ -7757,12 +7774,21 @@ 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: + 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( | ^~~~~~~~~~~~~~~~~~~~ +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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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 +[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 +[ 89%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 89%] Built target rxnTestCatch +[ 89%] Built target rdDeprotect [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o @@ -7775,19 +7801,34 @@ cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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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-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 +[ 90%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd 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../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 90%] Built target rdmolops [ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 [ 91%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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/usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 91%] Built target rdChemReactions -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT 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/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-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 92%] Built target rdChemReactions +[ 92%] Linking CXX executable testMolEnumerator +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so 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Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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 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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 -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/x86_64-linux-gnu/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/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_serialization.so @@ -7795,155 +7836,92 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 92%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= +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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +[ 94%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 95%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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'/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 95%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 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/usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 -[ 95%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 95%] Built target molFragmentTest -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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -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-x86_64-linux-gnu' -[ 95%] Built target molValidateTest -[ 95%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 95%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o +[ 94%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -7955,33 +7933,13 @@ 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/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: + 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 95%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 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, @@ -7992,24 +7950,13 @@ 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/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp:10: + 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("") | ^~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 95%] Built target molStandardizeTest -[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 97%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 97%] Built target molChargeTest -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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, @@ -8037,15 +7984,13 @@ 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/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:11: + 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-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.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, @@ -8060,21 +8005,83 @@ /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,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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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/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-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2022.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +[ 94%] Linking CXX executable molStandardizeSmallTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 +[ 94%] Linking CXX executable molNormalizeTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 97%] Built target ScaffoldNetwork -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend +[ 94%] Built target molStandardizeSmallTest +make -f 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molValidateTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 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../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 97%] Built target molValidateTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 97%] Built target molChargeTest +[ 97%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so 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/build/reproducible-path/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +[ 97%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 97%] Linking CXX executable molStandardizeTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 97%] Built target molStandardizeTest 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, @@ -8094,9 +8101,6 @@ /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, @@ -8114,64 +8118,69 @@ /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/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-x86_64-linux-gnu' -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -[ 98%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so -[ 98%] Linking CXX executable molStandardizeCatchTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 98%] Built target tautomerQueryTestCatch -[ 98%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so +/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( + | ^~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libcairo.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 98%] Built target molStandardizeCatchTest cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 98%] Built target MolDraw2D +[ 97%] Built target MolDraw2D make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend -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-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 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/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= +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-x86_64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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--color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' 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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +[ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT 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-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 -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +[ 97%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_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 -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_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 +[ 97%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 +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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 97%] Built target molStandardizeCatchTest 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, @@ -8186,10 +8195,42 @@ 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/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.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( | ^~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu/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-x86_64-linux-gnu' +[ 97%] Built target ScaffoldNetwork +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-x86_64-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 +[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 98%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 98%] Built target tautomerQueryTestCatch +[ 98%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 98%] Built target moldraw2DRxnTest1 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, @@ -8204,7 +8245,7 @@ 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/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: + from /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.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( | ^~~~~~~~~~~~~~~~~~~~ @@ -8218,63 +8259,56 @@ /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/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 99%] Built target rdTautomerQuery -[ 99%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 99%] Built target moldraw2DRxnTest1 [ 99%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 99%] Built target rdMolStandardize +[ 99%] Linking CXX executable testReaction +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 99%] Built target testReaction [ 99%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.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,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.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/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/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.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 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/x86_64-linux-gnu/libboost_serialization.so -[ 99%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 99%] Built target SubstructLibrary make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= -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-x86_64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu && /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-x86_64-linux-gnu /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +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-x86_64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +make[4]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202209.3/Code -I/build/reproducible-path/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_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 [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 99%] Built target testScaffoldNetwork -[ 99%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -[ 99%] Built target testReaction [ 99%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so /usr/lib/x86_64-linux-gnu/libpython3.11.so /usr/lib/x86_64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 99%] Built target rdScaffoldNetwork +[ 99%] Linking CXX executable testScaffoldNetwork +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 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, @@ -8293,6 +8327,8 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 99%] Built target testScaffoldNetwork 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, @@ -8316,11 +8352,6 @@ /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/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/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 99%] Built target substructLibraryCatchTest -[ 99%] Linking CXX executable substructLibraryTest -cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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-x86_64-linux-gnu' -[ 99%] 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, @@ -8348,10 +8379,15 @@ | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | numThreads); | ~~~~~~~~~~~ +[ 99%] Linking CXX executable substructLibraryTest +cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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 [ 99%] Linking CXX executable moldraw2DTest1 cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcoordgen.so /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/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/x86_64-linux-gnu/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/x86_64-linux-gnu/libcairo.so /usr/lib/x86_64-linux-gnu/libfreetype.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' +[ 99%] Built target substructLibraryTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' [ 99%] Built target moldraw2DTest1 [ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 @@ -13858,7 +13894,7 @@ /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 @@ -16339,10 +16375,10 @@ /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202209.3 PYTHONPATH=/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu//lib:" PYTHONPATH=/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/:/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu//lib:" dh_auto_test - cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15 + cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 make[2]: Entering directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j15 +/usr/bin/ctest --force-new-ctest-process --verbose -j16 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -16445,65 +16481,12 @@ 15: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/testTransforms 15: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry 15: Test timeout computed to be: 1500 -3: [03:04:10] Testing Github940: property dictionaries leaking memory -3: [03:04:10] 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 -5: [03:04:10] -5: ----------------------------------------- -5: [03:04:10] Finished: testPushAndPop() -5: [03:04:10] -5: ----------------------------------------- -5: [03:04:10] -5: ----------------------------------------- - 1/208 Test #4: testRDValue ............................ Passed 0.17 sec test 16 Start 16: testGrid 16: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/testGrid 16: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry 16: Test timeout computed to be: 1500 -7: [03:04:10] should not be silent -7: [03:04:10] should not be silent -7: [03:04:10] should not be silent -7: [03:04:10] should not be silent -7: [03:04:10] should not be silent -7: [03:04:10] should not be silent -7: [03:04:10] should not be silent -7: [03:04:10] should not be silent -7: [03:04:10] should not be silent -7: =============================================================================== -7: All tests passed (24 assertions in 2 test cases) -7: -8: 10, 11, 14, -8: t1: 10, 11, 14, -8: t2: 10, 11, 15, 17, -8: t1|t2: 10, 11, 14, 15, 17, -8: t1&t2: 10, 11, -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, - 2/208 Test #7: logTestsCatch .......................... Passed 0.16 sec -test 17 - Start 17: geometryTestsCatch - -17: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/geometryTestsCatch -17: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry -17: Test timeout computed to be: 1500 -8: except 1: core 1: RDKit 2D 1: @@ -16771,13 +16754,6 @@ 1: 9 5 1 0 1: M END 1: - 3/208 Test #9: testFPB ................................ Passed 0.16 sec -test 18 - Start 18: testPyGeometry - -18: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/testGeometry.py" -18: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap -18: Test timeout computed to be: 1500 1: core+sidechain 1: RDKit 2D 1: @@ -16870,37 +16846,6 @@ 1: 11 9 1 0 1: M END 1: -15: **************************************** -15: testPointND -15: **************************************** -15: testPointOps3D -15: **************************************** -15: testPointOps2D -15: **************************************** -15: test12D -15: ref1: 3.27461 3.83299 ref2: 0.128563 3.23326 -15: pt1: 0.971338 1.05963 pt2: 3.97058 0.423253 -15: **************************************** -15: test23D -15: **************************************** -15: test3MatMultiply -15: Pt1: 1 0 0 Pt2: 2 0 0 -15: -Pt1: -1 -0 -0 -15: tp1: 0 0 0 tp2: 0 0 0 -15: tp1: 0 0 0 tp2: 0 0 0 -15: tp1: 0 0 3 tp2: 0 0 3 -15: npt1: 0 0 3 npt2: 0 0 4 -15: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 -15: **************************************** -15: testFromQuaternion -15: **************************************** - 4/208 Test #15: testTransforms ......................... Passed 0.12 sec -test 19 - Start 19: testMatrices - -19: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/testMatrices -19: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics -19: Test timeout computed to be: 1500 1: core 1: RDKit 2D 1: @@ -16954,10 +16899,6 @@ 1: 5 7 1 0 1: M END 1: -19: [03:04:10] ----------------------------------------- -19: [03:04:10] Testing RDNumerics: vectors and matrices Code -19: [03:04:10] --------------------------------------- -19: [03:04:10] test1Vector 1: test1 1: RDKit 2D 1: @@ -17003,33 +16944,46 @@ 1: 2 5 1 0 1: M END 1: +3: [12:10:15] Testing Github940: property dictionaries leaking memory +3: [12:10:15] 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 +5: [12:10:15] +5: ----------------------------------------- +5: [12:10:15] Finished: testPushAndPop() +5: [12:10:15] +5: ----------------------------------------- +5: [12:10:15] +5: ----------------------------------------- 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -16: *********************************************************** -16: Testing Grid -16: --------------------------------- -16: testUniformGrid1 -16: -16: --------------------------------- -16: testUniformGrid2 -16: -16: --------------------------------- -16: testUniformGridPickling -16: -16: --------------------------------- -16: testGridOps -16: -16: --------------------------------- -16: testUniformGridIndexing -16: - 5/208 Test #16: testGrid ............................... Passed 0.10 sec -test 20 - Start 20: testConrec - -20: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/testConrec -20: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics -20: Test timeout computed to be: 1500 +7: [12:10:15] should not be silent +7: [12:10:15] should not be silent +7: [12:10:15] should not be silent +7: [12:10:15] should not be silent +7: [12:10:15] should not be silent +7: [12:10:15] should not be silent +7: [12:10:15] should not be silent +7: [12:10:15] should not be silent +7: [12:10:15] should not be silent +7: =============================================================================== +7: All tests passed (24 assertions in 2 test cases) +7: 8: 10, 11, 14, 8: t1: 10, 11, 14, 8: t2: 10, 11, 15, 17, @@ -17038,53 +16992,180 @@ 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 #6: dictTestsCatch ......................... Passed 0.26 sec +8: 10, 11, 14, +8: t1: 10, 11, 14, +8: t2: 10, 11, 15, 17, +8: t1|t2: 10, 11, 14, 15, 17, +8: t1&t2: 10, 11, +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 +15: **************************************** +15: testPointND +15: **************************************** +15: testPointOps3D +15: **************************************** +15: testPointOps2D +15: **************************************** +15: test12D +15: ref1: 2.04648 0.28939 ref2: 1.5362 0.781553 +15: pt1: 1.74909 4.01376 pt2: 1.88847 2.95937 +15: **************************************** +15: test23D +15: **************************************** +15: test3MatMultiply +15: Pt1: 1 0 0 Pt2: 2 0 0 +15: -Pt1: -1 -0 -0 +15: tp1: 0 0 0 tp2: 0 0 0 +15: tp1: 0 0 0 tp2: 0 0 0 +15: tp1: 0 0 3 tp2: 0 0 3 +15: npt1: 0 0 3 npt2: 0 0 4 +15: Pt1: 0 0 3 Pt2: 6.12323e-17 0 4 +15: **************************************** +15: testFromQuaternion +15: **************************************** + 1/208 Test #4: testRDValue ............................ Passed 0.30 sec +test 17 + Start 17: geometryTestsCatch + +17: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/geometryTestsCatch +17: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry +17: Test timeout computed to be: 1500 + 2/208 Test #6: dictTestsCatch ......................... Passed 0.27 sec +test 18 + Start 18: testPyGeometry + +18: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/Geometry/Wrap/testGeometry.py" +18: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Geometry/Wrap +18: Test timeout computed to be: 1500 + 3/208 Test #7: logTestsCatch .......................... Passed 0.26 sec +test 19 + Start 19: testMatrices + +19: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/testMatrices +19: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics +19: Test timeout computed to be: 1500 + 4/208 Test #8: testDataStructs ........................ Passed 0.27 sec +test 20 + Start 20: testConrec + +20: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/testConrec +20: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics +20: Test timeout computed to be: 1500 + 5/208 Test #9: testFPB ................................ Passed 0.26 sec test 21 Start 21: testAlignment 21: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment/testAlignment 21: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Alignment 21: Test timeout computed to be: 1500 -19: [03:04:10] --------------------------------------- -19: [03:04:10] test2Matrix - 7/208 Test #8: testDataStructs ........................ Passed 0.25 sec + 6/208 Test #10: testMultiFPB ........................... Passed 0.26 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-x86_64-linux-gnu/Code/Numerics/Alignment/Wrap 22: Test timeout computed to be: 1500 -19: [03:04:10] --------------------------------------- -19: [03:04:10] test3SquareMatrix -19: [03:04:10] --------------------------------------- -19: [03:04:10] test4SymmMatrix - 8/208 Test #19: testMatrices ........................... Passed 0.06 sec + 7/208 Test #15: testTransforms ......................... Passed 0.17 sec test 23 Start 23: testOptimizer 23: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer/testOptimizer 23: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/Numerics/Optimizer 23: Test timeout computed to be: 1500 - 9/208 Test #10: testMultiFPB ........................... Passed 0.22 sec +16: *********************************************************** +16: Testing Grid +16: --------------------------------- +16: testUniformGrid1 +16: +16: --------------------------------- +16: testUniformGrid2 +16: +16: --------------------------------- +16: testUniformGridPickling +16: +16: --------------------------------- +16: testGridOps +16: +16: --------------------------------- +16: testUniformGridIndexing +16: + 8/208 Test #16: testGrid ............................... Passed 0.17 sec test 24 Start 24: testUFFForceField -24: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField -24: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/UFF -24: Test timeout computed to be: 1500 +24: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/UFF/testUFFForceField +24: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/UFF +24: Test timeout computed to be: 1500 +17: =============================================================================== +17: All tests passed (50 assertions in 5 test cases) +17: + 9/208 Test #17: geometryTestsCatch ..................... Passed 0.11 sec +test 25 + Start 25: testMMFFForceField + +25: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +25: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF +25: Test timeout computed to be: 1500 +19: [12:10:16] ----------------------------------------- +19: [12:10:16] Testing RDNumerics: vectors and matrices Code +19: [12:10:16] --------------------------------------- +19: [12:10:16] test1Vector +19: [12:10:16] --------------------------------------- +19: [12:10:16] test2Matrix +19: [12:10:16] --------------------------------------- +19: [12:10:16] test3SquareMatrix +19: [12:10:16] --------------------------------------- +19: [12:10:16] test4SymmMatrix + 10/208 Test #19: testMatrices ........................... Passed 0.11 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-x86_64-linux-gnu/Code/ForceField/Wrap +26: Test timeout computed to be: 1500 +21: ----------------------------------------- +21: Testing Alignment Code +21: --------------------------------------- +21: testBasic +21: --------------------------------------- +21: testTriangle +21: --------------------------------------- +21: testFourPts +21: --------------------------------------- +21: testReflection +21: --------------------------------------- 23: ------------------------------------- 23: Testing linear search. 23: done 23: ------------------------------------- 23: Testing BFGS optimization. 23: done - 10/208 Test #23: testOptimizer .......................... Passed 0.01 sec -test 25 - Start 25: testMMFFForceField + 11/208 Test #23: testOptimizer .......................... Passed 0.06 sec +test 27 + Start 27: testDistGeom -25: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -25: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/ForceField/MMFF -25: Test timeout computed to be: 1500 +27: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom +27: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom +27: Test timeout computed to be: 1500 + 12/208 Test #21: testAlignment .......................... Passed 0.10 sec +test 28 + Start 28: pyDistGeom + +28: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py" +28: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap +28: Test timeout computed to be: 1500 +20: =============================================================================== +20: test cases: 1 | 1 passed +20: assertions: - none - +20: + 13/208 Test #20: testConrec ............................. Passed 0.13 sec +test 29 + Start 29: graphmolTest1 + +29: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 +29: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +29: Test timeout computed to be: 1500 24: ------------------------------------- 24: Unit tests for force field basics. 24: done @@ -17131,38 +17212,8 @@ 24: done 24: ------------------------------------- 24: Unit tests for all UFF constraint terms. -3: static boost any:0.273979 s -21: ----------------------------------------- -21: Testing Alignment Code -21: --------------------------------------- -21: testBasic -21: --------------------------------------- -21: testTriangle -21: --------------------------------------- -21: testFourPts -21: --------------------------------------- -21: testReflection -21: --------------------------------------- - 11/208 Test #21: testAlignment .......................... Passed 0.07 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-x86_64-linux-gnu/Code/ForceField/Wrap -26: Test timeout computed to be: 1500 25: ------------------------------------- 25: Official MMFF validation suite. -20: =============================================================================== -20: test cases: 1 | 1 passed -20: assertions: - none - -20: - 12/208 Test #20: testConrec ............................. Passed 0.13 sec -test 27 - Start 27: testDistGeom - -27: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom/testDistGeom -27: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom -27: Test timeout computed to be: 1500 27: *********************************************************** 27: test1 27: *********************************************************** @@ -17174,29 +17225,52 @@ 27: 1 1 1 0 27: *********************************************************** 27: -24: done -24: ------------------------------------- -24: Unit tests for copying UFF ForceFields. -24: done -24: ------------------------------------- -24: Unit test for UFF butane scan. -17: =============================================================================== -17: All tests passed (50 assertions in 5 test cases) -17: - 13/208 Test #17: geometryTestsCatch ..................... Passed 0.26 sec -test 28 - Start 28: pyDistGeom - -28: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py" -28: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DistGeom/Wrap -28: Test timeout computed to be: 1500 14/208 Test #27: testDistGeom ........................... Passed 0.08 sec -test 29 - Start 29: graphmolTest1 +test 30 + Start 30: graphmolcpTest -29: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTest1 -29: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -29: Test timeout computed to be: 1500 +30: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest +30: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +30: Test timeout computed to be: 1500 +3: static boost any:0.376127 s +30: +30: +30: +30: COPY + 15/208 Test #30: graphmolcpTest ......................... Passed 0.05 sec +test 31 + Start 31: graphmolqueryTest + +31: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest +31: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +31: Test timeout computed to be: 1500 +29: Atoms: +29: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 +29: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 +29: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 +29: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 +29: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 +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: [12:10:16] +29: +29: **** +29: Pre-condition Violation +29: getExplicitValence() called without call to calcExplicitValence() +29: Violation occurred on line 306 in file ./Code/GraphMol/Atom.cpp +29: Failed Expression: d_explicitValence > -1 +29: **** +29: +29: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 +29: Bonds: +29: 0 0->1 order: 1 conj?: 0 aromatic?: 0 +29: 1 1->2 order: 2 conj?: 0 aromatic?: 0 +29: 2 2->3 order: 1 conj?: 0 aromatic?: 0 +29: 3 0->4 order: 1 conj?: 0 aromatic?: 0 +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 1: cyclosporine a 1: RDKit 2D 1: @@ -17373,6 +17447,53 @@ 1: 46 3 1 0 1: M END 1: +29: [12:10:16] +29: +29: **** +29: Pre-condition Violation +29: bond already exists +29: Violation occurred on line 334 in file ./Code/GraphMol/RWMol.cpp +29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +29: **** +29: +29: [12:10:16] +29: +29: **** +29: Pre-condition Violation +29: bond already exists +29: Violation occurred on line 334 in file ./Code/GraphMol/RWMol.cpp +29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +29: **** +29: +29: [12:10:16] +29: +29: **** +29: Pre-condition Violation +29: attempt to add self-bond +29: Violation occurred on line 333 in file ./Code/GraphMol/RWMol.cpp +29: Failed Expression: atomIdx1 != atomIdx2 +29: **** +29: +29: [12:10:16] +29: +29: **** +29: Pre-condition Violation +29: bond already exists +29: Violation occurred on line 440 in file ./Code/GraphMol/ROMol.cpp +29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) +29: **** +29: +29: [12:10:16] +29: +29: **** +29: Pre-condition Violation +29: attempt to add self-bond +29: Violation occurred on line 438 in file ./Code/GraphMol/ROMol.cpp +29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() +29: **** +29: +29: [12:10:16] Explicit valence for atom # 0 B, 4, is greater than permitted +29: [12:10:16] Explicit valence for atom # 0 B, 5, is greater than permitted 1: single-double 1: RDKit 2D 1: @@ -17437,6 +17558,36 @@ 1: 9 10 1 0 1: M END 1: +31: [12:10:16] ---------------------- Test1 +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test2 +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test3 +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test4 +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test5 +31: [12:10:16] Done! +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test issue 2892580 +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test github issue 53: query molecules not matching [R] +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test queries using qualifiers instead of == +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test extra atom queries +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test extra bond queries +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test num heteroatom neighbor queries +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test atom type queries +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +31: [12:10:16] Done! +31: [12:10:16] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() 1: admntn 1: RDKit 2D 1: @@ -17465,81 +17616,15 @@ 1: 10 2 1 0 1: M END 1: -29: Atoms: -29: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 -29: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 -29: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 -29: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 -29: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 -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: [03:04:11] -29: -29: **** -29: Pre-condition Violation -29: getExplicitValence() called without call to calcExplicitValence() -29: Violation occurred on line 306 in file ./Code/GraphMol/Atom.cpp -29: Failed Expression: d_explicitValence > -1 -29: **** -29: -29: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 -29: Bonds: -29: 0 0->1 order: 1 conj?: 0 aromatic?: 0 -29: 1 1->2 order: 2 conj?: 0 aromatic?: 0 -29: 2 2->3 order: 1 conj?: 0 aromatic?: 0 -29: 3 0->4 order: 1 conj?: 0 aromatic?: 0 -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: [03:04:11] -29: -29: **** -29: Pre-condition Violation -29: bond already exists -29: Violation occurred on line 334 in file ./Code/GraphMol/RWMol.cpp -29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -29: **** -29: -29: [03:04:11] -29: -29: **** -29: Pre-condition Violation -29: bond already exists -29: Violation occurred on line 334 in file ./Code/GraphMol/RWMol.cpp -29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -29: **** -29: -29: [03:04:11] -29: -29: **** -29: Pre-condition Violation -29: attempt to add self-bond -29: Violation occurred on line 333 in file ./Code/GraphMol/RWMol.cpp -29: Failed Expression: atomIdx1 != atomIdx2 -29: **** -29: -29: [03:04:11] -29: -29: **** -29: Pre-condition Violation -29: bond already exists -29: Violation occurred on line 440 in file ./Code/GraphMol/ROMol.cpp -29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) -29: **** -29: -29: [03:04:11] -29: -29: **** -29: Pre-condition Violation -29: attempt to add self-bond -29: Violation occurred on line 438 in file ./Code/GraphMol/ROMol.cpp -29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() -29: **** -29: -29: [03:04:11] Explicit valence for atom # 0 B, 4, is greater than permitted -29: [03:04:11] Explicit valence for atom # 0 B, 5, is greater than permitted -29: [03:04:11] +31: [12:10:16] Done! + 16/208 Test #31: graphmolqueryTest ...................... Passed 0.05 sec +test 32 + Start 32: graphmolMolOpsTest + +32: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +32: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +32: Test timeout computed to be: 1500 +29: [12:10:16] 29: 29: **** 29: Post-condition Violation @@ -17548,12 +17633,25 @@ 29: Failed Expression: anum > -1 29: **** 29: -29: [03:04:11] ------------------------------------- -29: [03:04:11] Test github381: thread-safe initialization of the periodic table -29: [03:04:11] done -29: [03:04:11] ------------------------------------- -29: [03:04:11] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [03:04:11] +29: [12:10:16] ------------------------------------- +29: [12:10:16] Test github381: thread-safe initialization of the periodic table +24: done +24: ------------------------------------- +24: Unit tests for copying UFF ForceFields. + 17/208 Test #1: testCoordGen ........................... Passed 0.73 sec +test 33 + Start 33: graphmoltestChirality + +33: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality +33: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +33: Test timeout computed to be: 1500 +24: done +24: ------------------------------------- +24: Unit test for UFF butane scan. +29: [12:10:16] done +29: [12:10:16] ------------------------------------- +29: [12:10:16] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [12:10:16] 29: 29: **** 29: Pre-condition Violation @@ -17562,7 +17660,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [03:04:11] +29: [12:10:16] 29: 29: **** 29: Pre-condition Violation @@ -17571,10 +17669,10 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [03:04:11] done -29: [03:04:11] ------------------------------------- -29: [03:04:11] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [03:04:11] +29: [12:10:16] done +29: [12:10:16] ------------------------------------- +29: [12:10:16] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [12:10:16] 29: 29: **** 29: Pre-condition Violation @@ -17583,7 +17681,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [03:04:11] +29: [12:10:16] 29: 29: **** 29: Pre-condition Violation @@ -17592,207 +17690,64 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [03:04:11] done -29: [03:04:11] ------------------------------------- -29: [03:04:11] Test github1453: RWMol.clear() should reset the numBonds count. -29: [03:04:11] done -29: [03:04:11] ------------------------------------- -29: [03:04:11] Test range-based for loops. -29: [03:04:11] done -29: [03:04:11] ------------------------------------- -29: [03:04:11] Test github1642: Atom index type is too low for big molecules. - 15/208 Test #1: testCoordGen ........................... Passed 0.66 sec -test 30 - Start 30: graphmolcpTest - -30: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolcpTest -30: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -30: Test timeout computed to be: 1500 -30: -30: -30: -30: COPY - 16/208 Test #30: graphmolcpTest ......................... Passed 0.03 sec -test 31 - Start 31: graphmolqueryTest - -31: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolqueryTest -31: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -31: Test timeout computed to be: 1500 -31: [03:04:11] ---------------------- Test1 -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test2 -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test3 -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test4 -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test5 -31: [03:04:11] Done! -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test issue 2892580 -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test github issue 53: query molecules not matching [R] -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test queries using qualifiers instead of == -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test extra atom queries -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test extra bond queries -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test num heteroatom neighbor queries -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test atom type queries -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -31: [03:04:11] Done! -31: [03:04:11] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -31: [03:04:11] Done! - 17/208 Test #31: graphmolqueryTest ...................... Passed 0.03 sec -test 32 - Start 32: graphmolMolOpsTest - -32: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -32: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -32: Test timeout computed to be: 1500 -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -12: ...... -12: ---------------------------------------------------------------------- -12: Ran 6 tests in 0.016s -12: -12: OK +29: [12:10:16] done +29: [12:10:16] ------------------------------------- +29: [12:10:16] Test github1453: RWMol.clear() should reset the numBonds count. +29: [12:10:16] done +29: [12:10:16] ------------------------------------- +29: [12:10:16] Test range-based for loops. +29: [12:10:16] done +29: [12:10:16] ------------------------------------- +29: [12:10:16] Test github1642: Atom index type is too low for big molecules. 32: 1 1 2 32: 1 1 1 32: 2 1 0.75 32: path: 2 -24: done - 18/208 Test #24: testUFFForceField ...................... Passed 0.42 sec -test 33 - Start 33: graphmoltestChirality - -33: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestChirality -33: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -33: Test timeout computed to be: 1500 -13: ......... -13: ---------------------------------------------------------------------- -13: Ran 9 tests in 0.086s -13: -13: OK -32: [03:04:11] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. -32: [03:04:11] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. -32: [03:04:11] Explicit valence for atom # 0 B, 5, is greater than permitted -32: [03:04:11] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [03:04:11] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [03:04:11] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [03:04:11] Explicit valence for atom # 1 Si, 7, is greater than permitted -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.044s -14: -14: OK +32: [12:10:16] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. +32: [12:10:16] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. 33: -------------------------- 33: -------------------------- 33: C/C=C/C(C)Cl - 19/208 Test #14: pyFPB .................................. Passed 0.71 sec +32: [12:10:16] Explicit valence for atom # 0 B, 5, is greater than permitted +32: [12:10:16] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [12:10:16] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [12:10:16] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [12:10:16] Explicit valence for atom # 1 Si, 7, is greater than permitted +33: [12:10:16] Conflicting single bond directions around double bond at index 2. +33: [12:10:16] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [12:10:16] Conflicting single bond directions around double bond at index 4. +33: [12:10:16] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [12:10:16] Conflicting single bond directions around double bond at index 15. +33: [12:10:16] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [12:10:16] Conflicting single bond directions around double bond at index 2. +33: [12:10:16] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [12:10:16] Conflicting single bond directions around double bond at index 1. +33: [12:10:16] BondStereo set to STEREONONE and single bond directions set to NONE. +32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +33: -------------------------------------------------- + 18/208 Test #33: graphmoltestChirality .................. Passed 0.18 sec test 34 Start 34: graphmoltestPickler 34: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPickler 34: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 - 20/208 Test #12: pyDiscreteValueVect .................... Passed 0.74 sec -test 35 - Start 35: graphmoltestPicklerGlobalSetting - -35: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -35: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 - 21/208 Test #13: pySparseIntVect ........................ Passed 0.75 sec -test 36 - Start 36: graphmolIterTest - -36: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest -36: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing String Pickle Roundtrips. -33: [03:04:11] Conflicting single bond directions around double bond at index 2. -33: [03:04:11] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [03:04:11] Conflicting single bond directions around double bond at index 4. -33: [03:04:11] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [03:04:11] Conflicting single bond directions around double bond at index 15. -33: [03:04:11] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [03:04:11] Conflicting single bond directions around double bond at index 2. -33: [03:04:11] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [03:04:11] Conflicting single bond directions around double bond at index 1. -33: [03:04:11] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [03:04:11] done -22: EEE.. -22: ====================================================================== -22: ERROR: test1Basic (__main__.TestCase.test1Basic) -22: ---------------------------------------------------------------------- -22: Traceback (most recent call last): -22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 41, in test1Basic -22: refPts = np.zeros((2, 3), np.float) -22: ^^^^^^^^ -22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ -22: raise AttributeError(__former_attrs__[attr]) -22: AttributeError: module 'numpy' has no attribute 'float'. -22: `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. -22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: -22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -22: -22: ====================================================================== -22: ERROR: test2Weights (__main__.TestCase.test2Weights) -22: ---------------------------------------------------------------------- -22: Traceback (most recent call last): -22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 79, in test2Weights -22: np.float) -22: ^^^^^^^^ -22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ -22: raise AttributeError(__former_attrs__[attr]) -22: AttributeError: module 'numpy' has no attribute 'float'. -22: `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. -22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: -22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -22: -22: ====================================================================== -22: ERROR: test3tetra (__main__.TestCase.test3tetra) -22: ---------------------------------------------------------------------- -22: Traceback (most recent call last): -22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 109, in test3tetra -22: np.float) -22: ^^^^^^^^ -22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ -22: raise AttributeError(__former_attrs__[attr]) -22: AttributeError: module 'numpy' has no attribute 'float'. -22: `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. -22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: -22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -22: -22: ---------------------------------------------------------------------- -22: Ran 5 tests in 0.011s -22: -22: FAILED (errors=3) -22: Testing Alignment Wrapper code: - 22/208 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.06 sec -test 37 - Start 37: hanoiTest - -37: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest -37: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 -32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 - 23/208 Test #36: graphmolIterTest ....................... Passed 0.06 sec -test 38 - Start 38: graphmolMemTest1 - -38: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 -38: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +32: [12:10:16] non-ring atom 0 marked aromatic +32: [12:10:16] non-ring atom 0 marked aromatic +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing String Pickle Roundtrips. +32: [12:10:16] Conflicting single bond directions around double bond at index 17. +32: [12:10:16] BondStereo set to STEREONONE and single bond directions set to NONE. +32: starting ring finding +32: done +32: starting ring finding +32: done +32: starting ring finding +32: done +32: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +32: starting sanitization 28: EEEEEE 28: ====================================================================== 28: ERROR: test1SmoothPass (__main__.TestCase.test1SmoothPass) @@ -17882,124 +17837,79 @@ 28: Ran 6 tests in 0.003s 28: 28: FAILED (errors=6) - 24/208 Test #38: graphmolMemTest1 ....................... Passed 0.04 sec -test 39 - Start 39: resMolSupplierTest - -39: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest -39: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 -26: ...[03:04:11] Warning: molecule is tagged as 3D, but all Z coords are zero -32: [03:04:11] non-ring atom 0 marked aromatic -32: [03:04:11] non-ring atom 0 marked aromatic -33: -------------------------------------------------- - 25/208 Test #33: graphmoltestChirality .................. Passed 0.25 sec -test 40 - Start 40: molBundleTest - -40: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest -40: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 -18: ........... -18: ---------------------------------------------------------------------- -18: Ran 11 tests in 0.125s -18: -18: OK -18: Testing Geometry wrapper -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing reading existing pickle file (v2). -32: [03:04:11] Conflicting single bond directions around double bond at index 17. -32: [03:04:11] BondStereo set to STEREONONE and single bond directions set to NONE. -32: starting ring finding -32: done -32: starting ring finding -32: done -3: dynamic boost any:0.640281 s -26: [03:04:11] Molecule does not have explicit Hs. Consider calling AddHs() -32: starting ring finding -32: done -32: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -32: starting sanitization -26: [03:04:11] -26: -26: **** -26: Invariant Violation -26: bad direction in linearSearch -26: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h -26: Failed Expression: status >= 0 -26: **** -26: - 26/208 Test #22: pyAlignment ............................***Failed 0.71 sec -EEE.. -====================================================================== -ERROR: test1Basic (__main__.TestCase.test1Basic) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 41, in test1Basic - refPts = np.zeros((2, 3), np.float) - ^^^^^^^^ - File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) -AttributeError: module 'numpy' has no attribute 'float'. -`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 - -====================================================================== -ERROR: test2Weights (__main__.TestCase.test2Weights) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 79, in test2Weights - np.float) - ^^^^^^^^ - File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) -AttributeError: module 'numpy' has no attribute 'float'. -`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 - -====================================================================== -ERROR: test3tetra (__main__.TestCase.test3tetra) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 109, in test3tetra - np.float) - ^^^^^^^^ - File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) -AttributeError: module 'numpy' has no attribute 'float'. -`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 - ----------------------------------------------------------------------- -Ran 5 tests in 0.011s - -FAILED (errors=3) -Testing Alignment Wrapper code: - -test 41 - Start 41: testSGroup - -41: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup -41: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.081s -2: -2: OK 32: done 32: starting sanitization 32: done +13: ......... +13: ---------------------------------------------------------------------- +13: Ran 9 tests in 0.033s +13: +13: OK 32: starting ring finding 32: done 32: starting ring finding 32: done +12: ...... +12: ---------------------------------------------------------------------- +12: Ran 6 tests in 0.013s +12: +12: OK 32: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 - 27/208 Test #28: pyDistGeom .............................***Failed 0.60 sec +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing reading existing pickle file (v2). +32: [12:10:16] WARNING: not removing hydrogen atom with dummy atom neighbors +32: ------------------------------- +22: EEE.. +22: ====================================================================== +22: ERROR: test1Basic (__main__.TestCase.test1Basic) +22: ---------------------------------------------------------------------- +22: Traceback (most recent call last): +22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 41, in test1Basic +22: refPts = np.zeros((2, 3), np.float) +22: ^^^^^^^^ +22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ +22: raise AttributeError(__former_attrs__[attr]) +22: AttributeError: module 'numpy' has no attribute 'float'. +22: `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. +22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: +22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +22: +22: ====================================================================== +22: ERROR: test2Weights (__main__.TestCase.test2Weights) +22: ---------------------------------------------------------------------- +22: Traceback (most recent call last): +22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 79, in test2Weights +22: np.float) +22: ^^^^^^^^ +22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ +22: raise AttributeError(__former_attrs__[attr]) +22: AttributeError: module 'numpy' has no attribute 'float'. +22: `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. +22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: +22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +22: +22: ====================================================================== +22: ERROR: test3tetra (__main__.TestCase.test3tetra) +22: ---------------------------------------------------------------------- +22: Traceback (most recent call last): +22: File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 109, in test3tetra +22: np.float) +22: ^^^^^^^^ +22: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ +22: raise AttributeError(__former_attrs__[attr]) +22: AttributeError: module 'numpy' has no attribute 'float'. +22: `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. +22: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: +22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +22: +22: ---------------------------------------------------------------------- +22: Ran 5 tests in 0.007s +22: +22: FAILED (errors=3) +22: Testing Alignment Wrapper code: +32: [12:10:16] Explicit valence for atom # 0 N, 4, is greater than permitted + 19/208 Test #28: pyDistGeom .............................***Failed 0.62 sec EEEEEE ====================================================================== ERROR: test1SmoothPass (__main__.TestCase.test1SmoothPass) @@ -18090,33 +18000,34 @@ FAILED (errors=6) -test 42 - Start 42: test-valgrind - -42: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind -42: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 - 28/208 Test #40: molBundleTest .......................... Passed 0.07 sec -test 43 - Start 43: graphmolTestsCatch +test 35 + Start 35: graphmoltestPicklerGlobalSetting -43: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch -43: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 -32: [03:04:11] WARNING: not removing hydrogen atom with dummy atom neighbors -32: ------------------------------- -32: [03:04:11] Explicit valence for atom # 0 N, 4, is greater than permitted -3: static RDAny:0.056421 s - 29/208 Test #41: testSGroup ............................. Passed 0.08 sec -test 44 - Start 44: graphmolSGroupCatch +35: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +35: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 +18: ........... +18: ---------------------------------------------------------------------- +18: Ran 11 tests in 0.044s +18: +18: OK +18: Testing Geometry wrapper +32: [12:10:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [12:10:16] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +32: [12:10:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [12:10:16] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +32: [12:10:16] WARNING: not removing hydrogen atom with dummy atom neighbors +35: [12:10:16] done + 20/208 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.07 sec +test 36 + Start 36: graphmolIterTest -44: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch -44: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing combining molecules using pickles. +36: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolIterTest +36: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] 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 @@ -18133,48 +18044,49 @@ 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: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing Issue164: Roundtrip Pickle Failure. -32: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [03:04:11] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -32: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [03:04:11] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 30/208 Test #18: testPyGeometry ......................... Passed 0.88 sec -test 45 - Start 45: graphmolAdjustQueryCatch +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing Issue164: Roundtrip Pickle Failure. +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing Issue219: Pickle Failure with Conformations. +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing Issue220: Pickle problems with bond stereochemistry. +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing query serialization. + 21/208 Test #18: testPyGeometry ......................... Passed 0.87 sec +test 37 + Start 37: hanoiTest -45: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -45: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing Issue219: Pickle Failure with Conformations. -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing Issue220: Pickle problems with bond stereochemistry. -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing query serialization. -34: [03:04:11] C=[$(C=O)] -34: [03:04:11] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing radical handling in pickles. -34: [03:04:11] done -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing sf.net issue 2788233. -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing sf.net issue 3202580. +37: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/hanoiTest +37: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +34: [12:10:16] C=[$(C=O)] +34: [12:10:16] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing radical handling in pickles. +34: [12:10:16] done +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing sf.net issue 2788233. +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing sf.net issue 3202580. 34: mass! 13.0034 -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing sf.net issue 3316407. -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing sf.net issue 3496759. +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing sf.net issue 3316407. +34: [12:10:16] done +34: [12:10:16] ------------------------------------- +34: [12:10:16] Testing sf.net issue 3496759. +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.109s +14: +14: OK 34: smi match: *C *C 34: smi match: **=* **=* 34: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -18186,6 +18098,20 @@ 34: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 34: smi match: nnnOC=O nnnOC=O 34: smi match: *=C=N *=C=N + 22/208 Test #12: pyDiscreteValueVect .................... Passed 1.07 sec +test 38 + Start 38: graphmolMemTest1 + +38: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolMemTest1 +38: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 + 23/208 Test #13: pySparseIntVect ........................ Passed 1.08 sec +test 39 + Start 39: resMolSupplierTest + +39: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/resMolSupplierTest +39: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 34: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 34: smi match: SP(S)=S SP(S)=S 34: smi match: NP(N)(N)=O NP(N)(N)=O @@ -18195,13 +18121,6 @@ 34: smi match: * * 34: smi match: C=P C=P 34: smi match: CC(=N)Cl CC(=N)Cl - 31/208 Test #42: test-valgrind .......................... Passed 0.08 sec -test 46 - Start 46: chiralityTestsCatch - -46: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch -46: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 34: smi match: N=O N=O 34: smi match: ** ** 34: smi match: N=C=N N=C=N @@ -18237,6 +18156,69 @@ 34: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 34: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 34: smi match: cN(=O)~O cN(=O)~O + 24/208 Test #22: pyAlignment ............................***Failed 0.88 sec +EEE.. +====================================================================== +ERROR: test1Basic (__main__.TestCase.test1Basic) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 41, in test1Basic + refPts = np.zeros((2, 3), np.float) + ^^^^^^^^ + File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ + raise AttributeError(__former_attrs__[attr]) +AttributeError: module 'numpy' has no attribute 'float'. +`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 + +====================================================================== +ERROR: test2Weights (__main__.TestCase.test2Weights) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 79, in test2Weights + np.float) + ^^^^^^^^ + File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ + raise AttributeError(__former_attrs__[attr]) +AttributeError: module 'numpy' has no attribute 'float'. +`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 + +====================================================================== +ERROR: test3tetra (__main__.TestCase.test3tetra) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py", line 109, in test3tetra + np.float) + ^^^^^^^^ + File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ + raise AttributeError(__former_attrs__[attr]) +AttributeError: module 'numpy' has no attribute 'float'. +`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 + +---------------------------------------------------------------------- +Ran 5 tests in 0.007s + +FAILED (errors=3) +Testing Alignment Wrapper code: + +test 40 + Start 40: molBundleTest + +40: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/molBundleTest +40: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 + 25/208 Test #36: graphmolIterTest ....................... Passed 0.11 sec +test 41 + Start 41: testSGroup + +41: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/testSGroup +41: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 34: smi match: *[CH2]N1C(=O)CCC1=O *[CH2]N1C(=O)CCC1=O 34: smi match: N~NC=O N~NC=O 34: smi match: *=N~C *=N~C @@ -18248,35 +18230,6 @@ 34: smi match: *C=S *C=S 34: smi match: *N *N 34: smi match: *C(=C)C=O *C(=C)C=O -43: [03:04:11] WARNING: not removing hydrogen atom without neighbors -43: [03:04:11] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:04:11] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:04:11] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:04:11] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:04:11] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [03:04:11] Explicit valence for atom # 1 N, 6, is greater than permitted -43: [03:04:11] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [03:04:11] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [03:04:11] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [03:04:11] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [03:04:11] non-ring atom 2 marked aromatic -43: [03:04:11] non-ring atom 2 marked aromatic -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [03:04:11] Explicit valence for atom # 1 O, 3, is greater than permitted -43: [03:04:11] Explicit valence for atom # 4 F, 2, is greater than permitted -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 6 7 8 -43: [03:04:11] Explicit valence for atom # 1 C, 5, is greater than permitted -43: [03:04:11] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [03:04:11] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [03:04:11] WARNING: not removing hydrogen atom with wedged bond -43: [03:04:11] WARNING: not removing hydrogen atom without neighbors -43: [03:04:11] WARNING: not removing hydrogen atom without neighbors -32: [03:04:11] WARNING: not removing hydrogen atom with dummy atom neighbors 34: smi match: *C#C *C#C 34: smi match: N#CCO N#CCO 34: smi match: O=N(=O)CCO O=N(=O)CCO @@ -18301,18 +18254,8 @@ 34: smi match: CCCCCCC CCCCCCC 34: smi match: CN=O CN=O 34: smi match: CS(=O)(=O)O CS(=O)(=O)O -43: [03:04:11] WARNING: not removing hydrogen atom without neighbors -43: [03:04:11] WARNING: not removing hydrogen atom without neighbors -43: [03:04:11] Unreasonable formal charge on hydrogen # 0. 34: smi match: O=C1CCO1 O=C1CCO1 34: smi match: C=C(S)[SH]=O C=C(S)[SH]=O - 32/208 Test #2: pyCoordGen ............................. Passed 1.19 sec -test 47 - Start 47: canonTestsCatch - -47: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch -47: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 34: smi match: C=CCO C=CCO 34: smi match: C=CC=N C=CC=N 34: smi match: C=CC=O C=CC=O @@ -18335,6 +18278,13 @@ 34: smi match: C=NO C=NO 34: smi match: C=NOC=O C=NOC=O 34: smi match: C=N=O C=N=O + 26/208 Test #38: graphmolMemTest1 ....................... Passed 0.07 sec +test 42 + Start 42: test-valgrind + +42: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/test-valgrind +42: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 34: smi match: N#CS N#CS 34: smi match: *CN=O *CN=O 34: smi match: NCN NCN @@ -18377,186 +18327,6 @@ 34: smi match: *C(c)O *C(c)O 34: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 34: smi match: cS(=O)(=O)O cS(=O)(=O)O -43: [03:04:11] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [03:04:11] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: no atom -43: Violation occurred on line 183 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with a molecule -43: Violation occurred on line 184 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at->hasOwningMol() -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with this molecule -43: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: &at->getOwningMol() == this -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: no atom -43: Violation occurred on line 382 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with a molecule -43: Violation occurred on line 383 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at->hasOwningMol() -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with this molecule -43: Violation occurred on line 384 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: &at->getOwningMol() == this -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: no atom -43: Violation occurred on line 390 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with a molecule -43: Violation occurred on line 391 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: at->hasOwningMol() -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: atom not associated with this molecule -43: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: &at->getOwningMol() == this -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: null atom passed in -43: Violation occurred on line 406 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: atom_pin -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: cannot take ownership of an atom which already has an owner -43: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: cannot take ownership of an bond which already has an owner -43: Violation occurred on line 433 in file ./Code/GraphMol/ROMol.cpp -43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this -43: **** -43: -43: [03:04:11] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:04:11] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:04:11] WARNING: not removing hydrogen atom without neighbors -43: [03:04:11] Explicit valence for atom # 1 F greater than permitted -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: plain atoms have no Query -43: Violation occurred on line 625 in file ./Code/GraphMol/Atom.cpp -43: Failed Expression: 0 -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: plain atoms have no Query -43: Violation occurred on line 630 in file ./Code/GraphMol/Atom.cpp -43: Failed Expression: 0 -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: plain bonds have no Query -43: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp -43: Failed Expression: 0 -43: **** -43: -43: [03:04:11] -43: -43: **** -43: Pre-condition Violation -43: plain bonds have no query -43: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp -43: Failed Expression: 0 -43: **** -43: -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:04:11] Unusual charge on atom 0 number of radical electrons set to zero -43: [03:04:11] Unusual charge on atom 0 number of radical electrons set to zero -43: [03:04:11] Unusual charge on atom 0 number of radical electrons set to zero -43: [03:04:11] non-ring atom 0 marked aromatic -43: [03:04:11] non-ring atom 0 marked aromatic -43: =============================================================================== -43: All tests passed (1316 assertions in 75 test cases) -43: -44: =============================================================================== -44: All tests passed (120 assertions in 6 test cases) -44: - 33/208 Test #43: graphmolTestsCatch ..................... Passed 0.12 sec -test 48 - Start 48: moliteratorTestsCatch - -48: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch -48: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 - 34/208 Test #44: graphmolSGroupCatch .................... Passed 0.09 sec -test 49 - Start 49: testDepictor - -49: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor -49: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -49: Test timeout computed to be: 1500 34: smi match: *c1ccccn1=O *c1ccccn1=O 34: smi match: *c1ccccn1 *c1ccccn1 34: smi match: *c1nccccn1 *c1nccccn1 @@ -18575,6 +18345,18 @@ 34: smi match: N#CS N#CS 34: smi match: C=NO C=NO 34: smi match: C=N[SH]=N C=N[SH]=N +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.091s +2: +2: OK + 27/208 Test #40: molBundleTest .......................... Passed 0.05 sec +test 43 + Start 43: graphmolTestsCatch + +43: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolTestsCatch +43: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 34: smi match: O=C(S)S O=C(S)S 34: smi match: N=C(S)S N=C(S)S 34: smi match: N=C(=N)S N=C(=N)S @@ -18595,6 +18377,14 @@ 34: smi match: NN=O NN=O 34: smi match: NC(=O)S NC(=O)S 34: smi match: N#CS N#CS +24: done + 28/208 Test #24: testUFFForceField ...................... Passed 0.94 sec +test 44 + Start 44: graphmolSGroupCatch + +44: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolSGroupCatch +44: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 34: smi match: NC(=O)C(N)=O NC(=O)C(N)=O 34: smi match: c=N c=N 34: smi match: C1COCO1 C1COCO1 @@ -18619,6 +18409,20 @@ 34: smi match: C1CO1 C1CO1 34: smi match: *c1-c-c-ccN1 *c1-c-c-ccN1 34: smi match: *C(*)=C *C(*)=C + 29/208 Test #14: pyFPB .................................. Passed 1.17 sec +test 45 + Start 45: graphmolAdjustQueryCatch + +45: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +45: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 + 30/208 Test #42: test-valgrind .......................... Passed 0.06 sec +test 46 + Start 46: chiralityTestsCatch + +46: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/chiralityTestsCatch +46: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 34: smi match: N#[NH+] N#[NH+] 34: smi match: C#NO C#NO 34: smi match: OOO OOO @@ -18648,6 +18452,7 @@ 34: smi match: CC=CC(C)=O CC=CC(C)=O 34: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 34: smi match: C#CC#N C#CC#N +26: ...[12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero 34: smi match: C#CC=O C#CC=O 34: smi match: C#CC(=O)OCC C#CC(=O)OCC 34: smi match: C#CC=O C#CC=O @@ -18667,9 +18472,6 @@ 34: smi match: *C[SH](=O)=O *C[SH](=O)=O 34: smi match: * * 34: smi match: *1CC1 *1CC1 -48: =============================================================================== -48: All tests passed (8 assertions in 3 test cases) -48: 34: smi match: O=COC=O O=COC=O 34: smi match: N=C=O N=C=O 34: smi match: N=C=S N=C=S @@ -18680,6 +18482,13 @@ 34: smi match: *N#[NH+] *N#[NH+] 34: smi match: *S* *S* 34: smi match: ** ** + 31/208 Test #41: testSGroup ............................. Passed 0.12 sec +test 47 + Start 47: canonTestsCatch + +47: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/canonTestsCatch +47: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 34: smi match: *CC* *CC* 34: smi match: *O[SiH3] *O[SiH3] 34: smi match: *OS(*)~O *OS(*)~O @@ -18688,20 +18497,6 @@ 34: smi match: *[N+](=C)[O-] *[N+](=C)[O-] 34: smi match: * * 34: smi match: *C(*)NCN(*)* *C(*)NCN(*)* -47: 2 6 8 4 9 0 7 3 5 1 -47: 1 5 7 3 9 0 8 4 6 2 -47: 1 5 7 3 9 0 8 4 6 2 -47: 1 5 7 3 9 0 8 4 6 2 -47: =============================================================================== -47: All tests passed (47 assertions in 2 test cases) -47: - 35/208 Test #48: moliteratorTestsCatch .................. Passed 0.04 sec -test 50 - Start 50: depictorCatch - -50: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch -50: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor -50: Test timeout computed to be: 1500 34: smi match: *OCC#N *OCC#N 34: smi match: **C=C **C=C 34: smi match: C=C[O-] C=C[O-] @@ -18717,14 +18512,53 @@ 34: smi match: SS SS 34: smi match: [SH] [SH] 34: smi match: *C* *C* +43: [12:10:17] WARNING: not removing hydrogen atom without neighbors +43: [12:10:17] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:10:17] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:10:17] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 34: smi match: * * 34: smi match: C[nH3+] C[nH3+] 34: smi match: cC(=N)[NH2] cC(=N)[NH2] +43: [12:10:17] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:10:17] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [12:10:17] Explicit valence for atom # 1 N, 6, is greater than permitted +43: [12:10:17] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [12:10:17] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [12:10:17] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [12:10:17] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [12:10:17] non-ring atom 2 marked aromatic +43: [12:10:17] non-ring atom 2 marked aromatic +45: =============================================================================== +45: All tests passed (281 assertions in 10 test cases) +45: +46: [12:10:17] unable to set wavy bonds for double bonds: 3 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [12:10:17] Explicit valence for atom # 1 O, 3, is greater than permitted +43: [12:10:17] Explicit valence for atom # 4 F, 2, is greater than permitted +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 6 7 8 +43: [12:10:17] Explicit valence for atom # 1 C, 5, is greater than permitted +43: [12:10:17] WARNING: not removing hydrogen atom with dummy atom neighbors 34: smi match: O=CN[OH] O=CN[OH] 34: smi match: NN NN 34: smi match: * * 34: smi match: *OP(=O)O* *OP(=O)O* 34: smi match: * * +43: [12:10:17] WARNING: not removing hydrogen atom with dummy atom neighbors + 32/208 Test #45: graphmolAdjustQueryCatch ............... Passed 0.07 sec +test 48 + Start 48: moliteratorTestsCatch + +48: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/moliteratorTestsCatch +48: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 +43: [12:10:17] WARNING: not removing hydrogen atom with wedged bond +43: [12:10:17] WARNING: not removing hydrogen atom without neighbors +43: [12:10:17] WARNING: not removing hydrogen atom without neighbors 34: smi match: * * 34: smi match: * * 34: smi match: *N=C(*)* *N=C(*)* @@ -18737,6 +18571,120 @@ 34: smi match: C[OH] C[OH] 34: smi match: C[OH] C[OH] 34: smi match: C[OH] C[OH] +44: =============================================================================== +44: All tests passed (120 assertions in 6 test cases) +44: + 33/208 Test #44: graphmolSGroupCatch .................... Passed 0.09 sec +test 49 + Start 49: testDepictor + +49: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/testDepictor +49: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +49: Test timeout computed to be: 1500 +43: [12:10:17] WARNING: not removing hydrogen atom without neighbors +43: [12:10:17] WARNING: not removing hydrogen atom without neighbors +43: [12:10:17] Unreasonable formal charge on hydrogen # 0. +43: [12:10:17] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [12:10:17] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: no atom +43: Violation occurred on line 183 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with a molecule +43: Violation occurred on line 184 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at->hasOwningMol() +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with this molecule +43: Violation occurred on line 185 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: &at->getOwningMol() == this +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: no atom +43: Violation occurred on line 382 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with a molecule +43: Violation occurred on line 383 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at->hasOwningMol() +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with this molecule +43: Violation occurred on line 384 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: &at->getOwningMol() == this +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: no atom +43: Violation occurred on line 390 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with a molecule +43: Violation occurred on line 391 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: at->hasOwningMol() +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: atom not associated with this molecule +43: Violation occurred on line 392 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: &at->getOwningMol() == this +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: null atom passed in +43: Violation occurred on line 406 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: atom_pin +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: cannot take ownership of an atom which already has an owner +43: Violation occurred on line 407 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this +43: **** +43: 34: smi match: C[OH] C[OH] 34: smi match: C[CH]=O C[CH]=O 34: smi match: *=* *=* @@ -18744,13 +18692,6 @@ 34: smi match: C#C C#C 34: smi match: *[CH]C=C *[CH]C=C 34: smi match: cCC(=O)[OH] cCC(=O)[OH] - 36/208 Test #47: canonTestsCatch ........................ Passed 0.08 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-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap -51: Test timeout computed to be: 1500 34: smi match: *C(*)(*)C(=O)[OH] *C(*)(*)C(=O)[OH] 34: smi match: CC(=O)C(=O)[OH] CC(=O)C(=O)[OH] 34: smi match: C=CC(=O)[OH] C=CC(=O)[OH] @@ -18763,6 +18704,70 @@ 34: smi match: *C[OH] *C[OH] 34: smi match: ** ** 34: smi match: *C[OH] *C[OH] +46: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero + 34/208 Test #2: pyCoordGen ............................. Passed 1.47 sec +test 50 + Start 50: depictorCatch + +50: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor/depictorCatch +50: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Depictor +50: Test timeout computed to be: 1500 +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: cannot take ownership of an bond which already has an owner +43: Violation occurred on line 433 in file ./Code/GraphMol/ROMol.cpp +43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this +43: **** +43: +43: [12:10:17] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:10:17] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:10:17] WARNING: not removing hydrogen atom without neighbors +43: [12:10:17] Explicit valence for atom # 1 F greater than permitted +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: plain atoms have no Query +43: Violation occurred on line 625 in file ./Code/GraphMol/Atom.cpp +43: Failed Expression: 0 +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: plain atoms have no Query +43: Violation occurred on line 630 in file ./Code/GraphMol/Atom.cpp +43: Failed Expression: 0 +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: plain bonds have no Query +43: Violation occurred on line 206 in file ./Code/GraphMol/Bond.cpp +43: Failed Expression: 0 +43: **** +43: +43: [12:10:17] +43: +43: **** +43: Pre-condition Violation +43: plain bonds have no query +43: Violation occurred on line 227 in file ./Code/GraphMol/Bond.cpp +43: Failed Expression: 0 +43: **** +43: +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 34: smi match: *C(*)=O *C(*)=O 34: smi match: * * 34: smi match: *CC(=O)[OH] *CC(=O)[OH] @@ -18774,12 +18779,44 @@ 34: smi match: *c *c 34: smi match: **:*cF **:*cF 34: smi match: cB([OH])[OH] cB([OH])[OH] +46: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +46: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +48: =============================================================================== +48: All tests passed (8 assertions in 3 test cases) +48: 34: smi match: N~N~N N~N~N 34: smi match: *N=N* *N=N* 34: smi match: *CC[OH] *CC[OH] 34: smi match: *CC[OH] *CC[OH] 34: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] 34: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] +26: [12:10:17] Molecule does not have explicit Hs. Consider calling AddHs() +26: [12:10:17] +26: +26: **** +26: Invariant Violation +26: bad direction in linearSearch +26: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h +26: Failed Expression: status >= 0 +26: **** +26: +47: 2 6 8 4 9 0 7 3 5 1 +47: 1 5 7 3 9 0 8 4 6 2 +47: 1 5 7 3 9 0 8 4 6 2 +47: 1 5 7 3 9 0 8 4 6 2 +47: =============================================================================== +47: All tests passed (47 assertions in 2 test cases) +47: + 35/208 Test #47: canonTestsCatch ........................ Passed 0.08 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-x86_64-linux-gnu/Code/GraphMol/Depictor/Wrap +51: Test timeout computed to be: 1500 34: smi match: *CCC(=O)[OH] *CCC(=O)[OH] 34: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] 34: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O @@ -18799,9 +18836,50 @@ 34: smi match: *=* *=* 34: smi match: C1CO1 C1CO1 34: smi match: *OC(*)=O *OC(*)=O +46: =============================================================================== +46: All tests passed (1587 assertions in 50 test cases) +46: +43: [12:10:17] Unusual charge on atom 0 number of radical electrons set to zero +43: [12:10:17] Unusual charge on atom 0 number of radical electrons set to zero +43: [12:10:17] Unusual charge on atom 0 number of radical electrons set to zero +43: [12:10:17] non-ring atom 0 marked aromatic +43: [12:10:17] non-ring atom 0 marked aromatic +43: =============================================================================== +43: All tests passed (1316 assertions in 75 test cases) +43: +50: =============================================================================== +50: All tests passed (65 assertions in 4 test cases) +50: + 36/208 Test #43: graphmolTestsCatch ..................... Passed 0.18 sec +test 52 + Start 52: smiTest1 + +52: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 +52: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +52: Test timeout computed to be: 1500 + 37/208 Test #46: chiralityTestsCatch .................... Passed 0.15 sec +test 53 + Start 53: smiTest2 + +53: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 +53: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +53: Test timeout computed to be: 1500 + 38/208 Test #48: moliteratorTestsCatch .................. Passed 0.10 sec +test 54 + Start 54: cxsmilesTest + +54: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest +54: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +54: Test timeout computed to be: 1500 + 39/208 Test #50: depictorCatch .......................... Passed 0.10 sec +test 55 + Start 55: smaTest1 + +55: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +55: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse +55: Test timeout computed to be: 1500 34: smi match: * * 34: smi match: *O*[OH] *O*[OH] -46: [03:04:11] unable to set wavy bonds for double bonds: 3 34: smi match: COC(C)(C)O COC(C)(C)O 34: smi match: *[OH] *[OH] 34: smi match: ** ** @@ -18822,9 +18900,6 @@ 34: smi match: *N(=O)~O *N(=O)~O 34: smi match: N N 34: smi match: OC(=O)C(O)=O OC(=O)C(O)=O -46: [03:04:11] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [03:04:11] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [03:04:11] Warning: molecule is tagged as 3D, but all Z coords are zero 34: smi match: C=NO C=NO 34: smi match: O~O O~O 34: smi match: c[OH] c[OH] @@ -18848,9 +18923,6 @@ 34: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 34: smi match: *C(*)=S *C(*)=S 34: smi match: *OC(*)=S *OC(*)=S -46: [03:04:11] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [03:04:11] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [03:04:11] Warning: molecule is tagged as 3D, but all Z coords are zero 34: smi match: * * 34: smi match: C[SH] C[SH] 34: smi match: c[SH] c[SH] @@ -18858,200 +18930,206 @@ 34: smi match: * * 34: smi match: ***** ***** 34: smi match: NC(N)=O NC(N)=O -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing sf.net issue 280. -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing sf.net issue 285. -34: [03:04:11] done -34: [03:04:11] done -34: [03:04:11] done -34: [03:04:11] done -34: [03:04:11] done -34: [03:04:11] done -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing Github2441: Add RDProps interface to Conformers. -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing Issue2510: Pickle Confs as double. -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing loading pickled mols with conformers -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing conformer reading/writing options -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing property reading options -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing property reading options -34: [03:04:11] done -34: [03:04:11] ------------------------------------- -34: [03:04:11] Testing boost::serialization integration -34: [03:04:11] done -46: [03:04:11] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -46: [03:04:11] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -26: ......[03:04:11] Warning: molecule is tagged as 3D, but all Z coords are zero -45: =============================================================================== -45: All tests passed (281 assertions in 10 test cases) -45: - 37/208 Test #34: graphmoltestPickler .................... Passed 0.45 sec -test 52 - Start 52: smiTest1 - -52: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 -52: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -52: Test timeout computed to be: 1500 -50: =============================================================================== -50: All tests passed (65 assertions in 4 test cases) -50: -26: [03:04:11] Molecule does not have explicit Hs. Consider calling AddHs() -26: [03:04:11] -26: -26: **** -26: Invariant Violation -26: bad direction in linearSearch -26: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h -26: Failed Expression: status >= 0 -26: **** -26: - 38/208 Test #50: depictorCatch .......................... Passed 0.08 sec -test 53 - Start 53: smiTest2 - -53: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 -53: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -53: Test timeout computed to be: 1500 - 39/208 Test #45: graphmolAdjustQueryCatch ............... Passed 0.18 sec -test 54 - Start 54: cxsmilesTest - -54: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest -54: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -54: Test timeout computed to be: 1500 -46: =============================================================================== -46: All tests passed (1587 assertions in 50 test cases) -46: -53: [03:04:11] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -53: [03:04:11] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -53: [03:04:11] SMILES Parse Error: syntax error while parsing: - -53: [03:04:11] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -53: [03:04:11] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -53: [03:04:11] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -53: [03:04:11] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -53: [03:04:11] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -53: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -53: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -53: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -53: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -53: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -53: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -53: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 40/208 Test #46: chiralityTestsCatch .................... Passed 0.18 sec -test 55 - Start 55: smaTest1 - -55: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -55: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse -55: Test timeout computed to be: 1500 - 41/208 Test #53: smiTest2 ............................... Passed 0.03 sec +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing sf.net issue 280. +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing sf.net issue 285. +34: [12:10:17] done +34: [12:10:17] done +34: [12:10:17] done +34: [12:10:17] done +34: [12:10:17] done +34: [12:10:17] done +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing Github2441: Add RDProps interface to Conformers. +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing Issue2510: Pickle Confs as double. +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing loading pickled mols with conformers +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing conformer reading/writing options +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing property reading options +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing property reading options +34: [12:10:17] done +34: [12:10:17] ------------------------------------- +34: [12:10:17] Testing boost::serialization integration +34: [12:10:17] done + 40/208 Test #34: graphmoltestPickler .................... Passed 0.70 sec test 56 Start 56: smiTestCatch 56: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 56: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 56: Test timeout computed to be: 1500 -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] WARNING: not removing hydrogen atom without neighbors -52: [03:04:11] Invalid chiral specification on atom 0 -52: [03:04:11] Invalid chiral specification on atom 0 -52: [03:04:11] Invalid chiral specification on atom 0 -52: [03:04:11] Invalid chiral specification on atom 0 -52: [03:04:11] Invalid chiral specification on atom 0 -52: [03:04:11] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -52: [03:04:11] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' - 42/208 Test #54: cxsmilesTest ........................... Passed 0.07 sec +53: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +53: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +53: [12:10:17] SMILES Parse Error: syntax error while parsing: - +53: [12:10:17] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +53: [12:10:17] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +53: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +53: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +53: [12:10:17] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +53: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +53: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +53: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +53: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +53: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +53: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +53: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 41/208 Test #53: smiTest2 ............................... Passed 0.08 sec test 57 Start 57: nontetrahedralCatch 57: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 57: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 -56: [03:04:11] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -56: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -56: [03:04:11] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -56: [03:04:11] SMARTS Parse Error: unclosed ring for input: 'C1C' -56: [03:04:11] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -56: [03:04:11] SMARTS Parse Error: syntax error while parsing: C)foo -56: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -56: [03:04:11] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -56: [03:04:11] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -56: [03:04:11] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -57: [03:04:11] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:04:11] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:04:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:04:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:04:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:04:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:04:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:04:12] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:04:12] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -57: =============================================================================== -57: All tests passed (308 assertions in 9 test cases) -57: -56: [03:04:12] w block attempts to set wedging on bond 0 more than once. -56: [03:04:12] improperly formatted w block - 43/208 Test #57: nontetrahedralCatch .................... Passed 0.14 sec + 42/208 Test #54: cxsmilesTest ........................... Passed 0.08 sec test 58 Start 58: fileParsersTest1 58: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 58: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 58: Test timeout computed to be: 1500 -56: [03:04:12] atom 3 is not associated with bond 1 in w block -56: =============================================================================== -56: All tests passed (969 assertions in 49 test cases) -56: -3: dynamic RDAny:0.420352 s -3: static RDValue:1e-06 s - 44/208 Test #56: smiTestCatch ........................... Passed 0.20 sec +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] WARNING: not removing hydrogen atom without neighbors +52: [12:10:17] Invalid chiral specification on atom 0 +52: [12:10:17] Invalid chiral specification on atom 0 +52: [12:10:17] Invalid chiral specification on atom 0 +52: [12:10:17] Invalid chiral specification on atom 0 +52: [12:10:17] Invalid chiral specification on atom 0 +56: [12:10:17] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +56: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +56: [12:10:17] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +56: [12:10:17] SMARTS Parse Error: unclosed ring for input: 'C1C' +56: [12:10:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +56: [12:10:17] SMARTS Parse Error: syntax error while parsing: C)foo +56: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +56: [12:10:17] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +56: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +56: [12:10:17] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +52: [12:10:17] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +52: [12:10:17] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +57: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [12:10:17] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [12:10:17] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +57: =============================================================================== +57: All tests passed (308 assertions in 9 test cases) +57: + 43/208 Test #57: nontetrahedralCatch .................... Passed 0.14 sec test 59 Start 59: testMolSupplier 59: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 59: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 59: Test timeout computed to be: 1500 -26: ... -26: ---------------------------------------------------------------------- -26: Ran 12 tests in 0.638s +58: *************************************** +58: *************************************** +56: [12:10:17] w block attempts to set wedging on bond 0 more than once. +56: [12:10:17] improperly formatted w block +56: [12:10:17] atom 3 is not associated with bond 1 in w block +56: =============================================================================== +56: All tests passed (969 assertions in 49 test cases) +56: + 44/208 Test #56: smiTestCatch ........................... Passed 0.20 sec +test 60 + Start 60: testGeneralFileReader + +60: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +60: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +60: Test timeout computed to be: 1500 +59: [12:10:17] +59: ----------------------------------------- +60: [12:10:17] +60: ----------------------------------------- +60: [12:10:17] Finished: testDetermineFormat() +60: [12:10:17] ----------------------------------------- +60: +60: [12:10:17] +60: ----------------------------------------- +26: ......[12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +26: [12:10:17] Molecule does not have explicit Hs. Consider calling AddHs() +26: [12:10:17] 26: -26: OK +26: **** +26: Invariant Violation +26: bad direction in linearSearch +26: Violation occurred on line 240 in file ./Code/Numerics/Optimizer/BFGSOpt.h +26: Failed Expression: status >= 0 +26: **** +26: +58: [12:10:17] bond with order 0 found on line 7. This is not part of the MDL specification. +58: [12:10:17] unrecognized query bond type, 9, found on line 7. Using an "any" query. +60: [12:10:17] Finished: testSdf() +60: [12:10:17] ----------------------------------------- +60: +60: [12:10:17] +60: ----------------------------------------- +55: [12:10:17] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +55: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +55: [12:10:17] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +55: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +59: [12:10:17] +59: +59: **** +59: Invariant Violation +59: bad prop value +59: Violation occurred on line 157 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +59: Failed Expression: nSwaps < 2 +59: **** +59: +55: [12:10:17] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +55: [12:10:17] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 52: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -3: dynamic RDValue:0.049108 s -59: [03:04:12] -59: ----------------------------------------- -3: deleted! -55: [03:04:12] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -55: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -55: [03:04:12] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -55: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -55: [03:04:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -55: [03:04:12] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +60: [12:10:17] Finished: testSmi() +60: [12:10:17] ----------------------------------------- +60: +60: [12:10:17] +60: ----------------------------------------- + 45/208 Test #55: smaTest1 ............................... Passed 0.40 sec +test 61 + Start 61: testMultithreadedMolSupplier + +61: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +61: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +61: Test timeout computed to be: 1500 +61: [12:10:17] +61: ----------------------------------------- +58: [12:10:17] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +58: [12:10:17] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +58: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:17] Warning: molecule is tagged as 3D, but all Z coords are zero 52: smi: ClC1CCCCC1 52: smi: ClC1CCCCC1 52: smi: ClC1CCCCC1Br @@ -19060,201 +19138,272 @@ 52: smi: c1cc[nH]c1 52: smi: c1cc[nH]c1 52: smi: c1cc[pH]c1 - 45/208 Test #55: smaTest1 ............................... Passed 0.28 sec -test 60 - Start 60: testGeneralFileReader - -60: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -60: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -60: Test timeout computed to be: 1500 52: CbC(aC)aC 52: CaC(bC)aC 52: CbC(bC)aC 52: O.C -3: [03:04:12] ------------------------------------- -3: [03:04:12] Testing String Pickle Roundtrips. -3: [03:04:12] done +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 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 -3: [03:04:12] ------------------------------------- -3: [03:04:12] Testing conversion of vect to string. -3: [03:04:12] done -3: [03:04:12] ------------------------------------- -3: [03:04:12] Testing returning const references. -3: [03:04:12] any cast -3: [03:04:12] done: 0.001336 300000 -3: [03:04:12] copy -3: [03:04:12] done: 0.001247 300000 -3: [03:04:12] ref -52: [03:04:12] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -52: [03:04:12] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -52: [03:04:12] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -52: [03:04:12] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -52: [03:04:12] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -3: [03:04:12] done: 0.001396 300000 -3: [03:04:12] dict -60: [03:04:12] -60: ----------------------------------------- -60: [03:04:12] Finished: testDetermineFormat() -60: [03:04:12] ----------------------------------------- -60: -60: [03:04:12] -60: ----------------------------------------- -52: [03:04:12] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -3: [03:04:12] done: 0.005207 300000 -3: [03:04:12] ref with hasVal -3: [03:04:12] done: 0.002235 300000 -3: [03:04:12] done -3: [03:04:12] ------------------------------------- -3: [03:04:12] Testing dict update. -3: [03:04:12] done -52: [03:04:12] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [03:04:12] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [03:04:12] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [03:04:12] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [03:04:12] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [03:04:12] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [03:04:12] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [03:04:12] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [03:04:12] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [12:10:17] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +52: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +52: [12:10:17] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +52: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +52: [12:10:17] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +52: [12:10:17] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +58: check isomorphism +49: [12:10:17] Warning: stereochemistry around double bond may be incorrect in depiction. +52: [12:10:17] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [12:10:17] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [12:10:17] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [12:10:17] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [12:10:17] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [12:10:17] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [12:10:17] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [12:10:17] 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: [03:04:12] SMILES Parse Error: extra close parentheses while parsing: C) -52: [03:04:12] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 46/208 Test #52: smiTest1 ............................... Passed 0.36 sec -test 61 - Start 61: testMultithreadedMolSupplier - -61: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -61: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -61: Test timeout computed to be: 1500 -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! - 47/208 Test #3: testDict ............................... Passed 1.69 sec +52: [12:10:17] SMILES Parse Error: extra close parentheses while parsing: C) +52: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 46/208 Test #52: smiTest1 ............................... Passed 0.58 sec test 62 Start 62: testMolWriter 62: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 62: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 62: Test timeout computed to be: 1500 - 48/208 Test #26: pyForceFieldConstraints ................ Passed 1.33 sec +26: ... +26: ---------------------------------------------------------------------- +26: Ran 12 tests in 0.960s +26: +26: OK +59: [12:10:17] Finished: testMolSup() +59: [12:10:17] ----------------------------------------- +59: +59: [12:10:17] ----------------------------------------- +59: [12:10:17] Finished: testRandMolSup() +59: [12:10:17] ----------------------------------------- +59: +59: [12:10:17] ----------------------------------------- + 47/208 Test #49: testDepictor ........................... Passed 0.69 sec test 63 Start 63: testTplParser 63: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 63: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 63: Test timeout computed to be: 1500 -61: [03:04:12] -61: ----------------------------------------- -58: *************************************** -58: *************************************** -60: [03:04:12] Finished: testSdf() -60: [03:04:12] ----------------------------------------- +60: [12:10:17] Finished: testMae() +60: [12:10:17] ----------------------------------------- 60: -60: [03:04:12] +60: [12:10:17] 60: ----------------------------------------- -32: [03:04:12] Maximum BFS search size exceeded. -32: This is likely due to a highly symmetric fused ring system. -59: [03:04:12] -59: -59: **** -59: Invariant Violation -59: bad prop value -59: Violation occurred on line 157 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -59: Failed Expression: nSwaps < 2 -59: **** -59: - 49/208 Test #63: testTplParser .......................... Passed 0.05 sec +60: [12:10:17] Finished: testTdt() +60: [12:10:17] ----------------------------------------- +60: + 48/208 Test #60: testGeneralFileReader .................. Passed 0.36 sec test 64 Start 64: testMol2ToMol 64: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 64: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 64: Test timeout computed to be: 1500 -60: [03:04:12] Finished: testSmi() -60: [03:04:12] ----------------------------------------- -60: -60: [03:04:12] -60: ----------------------------------------- -58: [03:04:12] bond with order 0 found on line 7. This is not part of the MDL specification. -58: [03:04:12] unrecognized query bond type, 9, found on line 7. Using an "any" query. -59: [03:04:12] Finished: testMolSup() -59: [03:04:12] ----------------------------------------- +51: ....E..... +51: ====================================================================== +51: ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) +51: ---------------------------------------------------------------------- +51: Traceback (most recent call last): +51: File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D +51: dmat3D = getDistMat(mol) +51: ^^^^^^^^^^^^^^^ +51: File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 31, in getDistMat +51: res = np.zeros(nl, np.float) +51: ^^^^^^^^ +51: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ +51: raise AttributeError(__former_attrs__[attr]) +51: AttributeError: module 'numpy' has no attribute 'float'. +51: `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. +51: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: +51: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations +51: +51: ---------------------------------------------------------------------- +51: Ran 10 tests in 0.326s +51: +51: FAILED (errors=1) +59: [12:10:17] Finished: testSmilesSup() +59: [12:10:17] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testRandMolSup() -59: [03:04:12] ----------------------------------------- +59: [12:10:17] ----------------------------------------- +59: [12:10:17] ------------------------------------------------------ +59: [12:10:17] SMILES Parse Error: syntax error while parsing: fail +59: [12:10:17] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +59: [12:10:17] ERROR: Smiles parse error on line 3 +59: [12:10:17] ERROR: Cannot create molecule from : 'fail' +59: [12:10:17] ------------------------------------------------------ +59: [12:10:17] ------------------------------------------------------ +59: [12:10:17] >>> This may result in an infinite loop. It should finish almost immediately: +59: [12:10:17] <<< done. +59: [12:10:17] Finished: testSmilesSupFromText() +59: [12:10:17] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -58: [03:04:12] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -58: [03:04:12] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -58: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -49: [03:04:12] Warning: stereochemistry around double bond may be incorrect in depiction. -60: [03:04:12] Finished: testMae() -60: [03:04:12] ----------------------------------------- -60: -60: [03:04:12] -60: ----------------------------------------- -60: [03:04:12] Finished: testTdt() -60: [03:04:12] ----------------------------------------- -60: - 50/208 Test #64: testMol2ToMol .......................... Passed 0.17 sec +59: [12:10:17] ----------------------------------------- +32: [12:10:17] Maximum BFS search size exceeded. +32: This is likely due to a highly symmetric fused ring system. + 49/208 Test #63: testTplParser .......................... Passed 0.10 sec test 65 Start 65: testSequence 65: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testSequence 65: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 65: Test timeout computed to be: 1500 -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 - 51/208 Test #60: testGeneralFileReader .................. Passed 0.31 sec +59: [12:10:17] Finished: testSmilesWriter() +59: [12:10:17] ----------------------------------------- +59: +59: [12:10:17] ----------------------------------------- +3: dynamic boost any:0.82938 s + 50/208 Test #51: pyDepictor .............................***Failed 0.80 sec +....E..... +====================================================================== +ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D + dmat3D = getDistMat(mol) + ^^^^^^^^^^^^^^^ + File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 31, in getDistMat + res = np.zeros(nl, np.float) + ^^^^^^^^ + File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ + raise AttributeError(__former_attrs__[attr]) +AttributeError: module 'numpy' has no attribute 'float'. +`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 + +---------------------------------------------------------------------- +Ran 10 tests in 0.326s + +FAILED (errors=1) + test 66 Start 66: testExtendedStereoParsing 66: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 66: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 66: Test timeout computed to be: 1500 -58: check isomorphism - 52/208 Test #49: testDepictor ........................... Passed 0.74 sec +59: [12:10:18] Finished: testSDWriter() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testSDSupplierEnding() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testSuppliersEmptyFile() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testCisTrans() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- + 51/208 Test #64: testMol2ToMol .......................... Passed 0.14 sec test 67 Start 67: fileParsersCatchTest 67: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 67: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 -59: [03:04:12] Finished: testSmilesSup() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] Finished: testStereoRound() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testIssue226() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testTDTSupplier1() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- + 52/208 Test #26: pyForceFieldConstraints ................ Passed 1.85 sec +test 68 + Start 68: testPropertyLists + +68: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +68: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +68: Test timeout computed to be: 1500 +59: [12:10:18] Finished: testTDTSupplier2() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testTDTSupplier3() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] ------------------------------------------------------ -59: [03:04:12] SMILES Parse Error: syntax error while parsing: fail -59: [03:04:12] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -59: [03:04:12] ERROR: Smiles parse error on line 3 -59: [03:04:12] ERROR: Cannot create molecule from : 'fail' -59: [03:04:12] ------------------------------------------------------ -59: [03:04:12] ------------------------------------------------------ -59: [03:04:12] >>> This may result in an infinite loop. It should finish almost immediately: -59: [03:04:12] <<< done. -59: [03:04:12] Finished: testSmilesSupFromText() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testSDSupplierFromText() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testSmilesWriter() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] ----------------------------------------- +59: [12:10:18] ERROR: Problems encountered parsing data fields +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] ERROR: Problems encountered parsing data fields +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Spurious data before the first property will be ignored +59: [12:10:18] Property will be truncated after the first blank line +59: [12:10:18] Property will be truncated after the first blank line +59: [12:10:18] Property will be truncated after the first blank line +59: [12:10:18] Finished: testSDSupplierStrLax1() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- +59: [12:10:18] ----------------------------------------- +59: [12:10:18] ERROR: Problems encountered parsing data fields +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Property will be truncated after the first blank line +59: [12:10:18] Finished: testSDSupplierStrLax2() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] ERROR: Problems encountered parsing data fields +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] ERROR: Problems encountered parsing data fields +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Spurious data before the first property will be ignored +59: [12:10:18] Property will be truncated after the first blank line +59: [12:10:18] Property will be truncated after the first blank line +59: [12:10:18] Property will be truncated after the first blank line +59: [12:10:18] Finished: testSDSupplierFromTextStrLax1() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] ERROR: Problems encountered parsing data fields +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Property will be truncated after the first blank line +59: [12:10:18] Finished: testSDSupplierFromTextStrLax2() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testIssue265() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] ERROR: End of data field name not found +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Explicit valence for atom # 0 F, 2, is greater than permitted +59: [12:10:18] ERROR: Could not sanitize molecule ending on line 16 +59: [12:10:18] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +59: [12:10:18] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] ERROR: Bond line too short: 'M END' on line 18 +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Finished: testSDErrorHandling() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- 65: Sequence: GREG 65: HELM: PEPTIDE1{G.R.E.G}$$$$ 65: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -19752,6 +19901,25 @@ 65: CONECT 163 164 164 170 65: CONECT 165 166 65: CONECT 166 167 + 53/208 Test #66: testExtendedStereoParsing .............. Passed 0.06 sec +test 69 + Start 69: XYZFileParserCatchTest + +69: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest +69: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers +69: Test timeout computed to be: 1500 +59: [12:10:18] Finished: testIssue381() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testSetStreamIndices() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testMixIterAndRandom() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- 65: CONECT 167 168 168 169 65: CONECT 170 171 65: CONECT 171 172 174 @@ -20239,164 +20407,41 @@ 65: CONECT 27 28 28 29 65: END 65: - 53/208 Test #65: testSequence ........................... Passed 0.08 sec -test 68 - Start 68: testPropertyLists - -68: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -68: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -68: Test timeout computed to be: 1500 -59: [03:04:12] Finished: testSDWriter() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testSDSupplierEnding() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- - 54/208 Test #66: testExtendedStereoParsing .............. Passed 0.08 sec -test 69 - Start 69: XYZFileParserCatchTest - -69: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest -69: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers -69: Test timeout computed to be: 1500 -59: [03:04:12] Finished: testSuppliersEmptyFile() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testCisTrans() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testStereoRound() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testIssue226() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testTDTSupplier1() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testTDTSupplier2() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testTDTSupplier3() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testSDSupplierFromText() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] ERROR: Problems encountered parsing data fields -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] ERROR: Problems encountered parsing data fields -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] Spurious data before the first property will be ignored -59: [03:04:12] Property will be truncated after the first blank line -59: [03:04:12] Property will be truncated after the first blank line -59: [03:04:12] Property will be truncated after the first blank line -59: [03:04:12] Finished: testSDSupplierStrLax1() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] ERROR: Problems encountered parsing data fields -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] Property will be truncated after the first blank line -59: [03:04:12] Finished: testSDSupplierStrLax2() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] ERROR: Problems encountered parsing data fields -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] ERROR: Problems encountered parsing data fields -59: [03:04:12] ERROR: moving to the beginning of the next molecule -68: =============================================================================== -68: All tests passed (94 assertions in 4 test cases) -68: -59: [03:04:12] Spurious data before the first property will be ignored -59: [03:04:12] Property will be truncated after the first blank line -59: [03:04:12] Property will be truncated after the first blank line -59: [03:04:12] Property will be truncated after the first blank line -59: [03:04:12] Finished: testSDSupplierFromTextStrLax1() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] ERROR: Problems encountered parsing data fields -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] Property will be truncated after the first blank line -59: [03:04:12] Finished: testSDSupplierFromTextStrLax2() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testIssue265() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] ERROR: End of data field name not found -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] Explicit valence for atom # 0 F, 2, is greater than permitted -59: [03:04:12] ERROR: Could not sanitize molecule ending on line 16 -59: [03:04:12] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -59: [03:04:12] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] ERROR: Bond line too short: 'M END' on line 18 -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] Finished: testSDErrorHandling() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- - 55/208 Test #68: testPropertyLists ...................... Passed 0.05 sec + 54/208 Test #65: testSequence ........................... Passed 0.13 sec test 70 Start 70: cdxmlParserCatchTest 70: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 70: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 -59: [03:04:12] Finished: testIssue381() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -62: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero -59: [03:04:12] Finished: testSetStreamIndices() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testMixIterAndRandom() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -67: [03:04:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -67: [03:04:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -67: [03:04:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [03:04:12] SGroup 1 is invalid and will be ignored -67: [03:04:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -67: [03:04:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [03:04:12] SGroup 1 is invalid and will be ignored -67: [03:04:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -67: [03:04:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -67: [03:04:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -67: [03:04:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -67: [03:04:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [03:04:12] SGroup 1 is invalid and will be ignored -67: [03:04:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -67: [03:04:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -67: [03:04:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [03:04:12] SGroup 1 is invalid and will be ignored 59: build: -59: [03:04:12] Finished: testRemoveHs() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] Finished: testRemoveHs() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -67: [03:04:12] SGroup 3 referenced on line 40 not found. -67: [03:04:12] +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testGetItemText() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +67: [12:10:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +67: [12:10:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +67: [12:10:18] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [12:10:18] SGroup 1 is invalid and will be ignored +67: [12:10:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +67: [12:10:18] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [12:10:18] SGroup 1 is invalid and will be ignored +67: [12:10:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +67: [12:10:18] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +67: [12:10:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +67: [12:10:18] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +67: [12:10:18] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [12:10:18] SGroup 1 is invalid and will be ignored +67: [12:10:18] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +67: [12:10:18] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +67: [12:10:18] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [12:10:18] SGroup 1 is invalid and will be ignored +67: [12:10:18] SGroup 3 referenced on line 40 not found. +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20405,8 +20450,8 @@ 67: Failed Expression: !d_bonds.empty() 67: **** 67: -67: [03:04:12] SGroup 3 referenced on line 40 not found. -67: [03:04:12] +67: [12:10:18] SGroup 3 referenced on line 40 not found. +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20415,13 +20460,23 @@ 67: Failed Expression: !d_bonds.empty() 67: **** 67: -67: [03:04:12] no bonds -67: [03:04:12] SGroup 1 is invalid and will be ignored -67: [03:04:12] SGroup line too short: 'M SBV 1 6' on line 42 -67: [03:04:12] SGroup 1 is invalid and will be ignored -67: [03:04:12] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -67: [03:04:12] SGroup 2 is invalid and will be ignored -67: [03:04:12] +67: [12:10:18] no bonds +67: [12:10:18] SGroup 1 is invalid and will be ignored +67: [12:10:18] SGroup line too short: 'M SBV 1 6' on line 42 +67: [12:10:18] SGroup 1 is invalid and will be ignored +68: =============================================================================== +68: All tests passed (94 assertions in 4 test cases) +68: + 55/208 Test #68: testPropertyLists ...................... Passed 0.09 sec +test 71 + Start 71: testSubstructMatch + +71: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +71: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +71: Test timeout computed to be: 1500 +67: [12:10:18] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +67: [12:10:18] SGroup 2 is invalid and will be ignored +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20430,7 +20485,7 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20439,8 +20494,8 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] multiple bonds with same bookmark -67: [03:04:12] +67: [12:10:18] multiple bonds with same bookmark +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20449,9 +20504,9 @@ 67: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 67: **** 67: -67: [03:04:12] bond is not part of the SubstanceGroup -67: [03:04:12] SGroup 2 is invalid and will be ignored -67: [03:04:12] +67: [12:10:18] bond is not part of the SubstanceGroup +67: [12:10:18] SGroup 2 is invalid and will be ignored +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20460,7 +20515,7 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20469,11 +20524,11 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] multiple atoms with same bookmark -67: [03:04:12] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -67: [03:04:12] SGroup 2 is invalid and will be ignored -67: [03:04:12] WARNING: final character of V3000 array is not ')' -67: [03:04:12] +67: [12:10:18] multiple atoms with same bookmark +67: [12:10:18] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +67: [12:10:18] SGroup 2 is invalid and will be ignored +67: [12:10:18] WARNING: final character of V3000 array is not ')' +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20482,8 +20537,8 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] WARNING: final character of V3000 array is not ')' -67: [03:04:12] +67: [12:10:18] WARNING: final character of V3000 array is not ')' +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20492,16 +20547,10 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] multiple bonds with same bookmark -67: [03:04:12] SGroup 1 is invalid and will be ignored -62: [03:04:12] bond with order 0 found on line 11. This is not part of the MDL specification. -62: [03:04:12] bond with order 0 found on line 16. This is not part of the MDL specification. -59: [03:04:12] Finished: testGetItemText() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -67: [03:04:12] WARNING: final character of V3000 array is not ')' -67: [03:04:12] +67: [12:10:18] multiple bonds with same bookmark +67: [12:10:18] SGroup 1 is invalid and will be ignored +67: [12:10:18] WARNING: final character of V3000 array is not ')' +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20510,8 +20559,8 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] WARNING: final character of V3000 array is not ')' -67: [03:04:12] +67: [12:10:18] WARNING: final character of V3000 array is not ')' +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20520,9 +20569,9 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] multiple atoms with same bookmark -67: [03:04:12] SGroup 1 is invalid and will be ignored -67: [03:04:12] +67: [12:10:18] multiple atoms with same bookmark +67: [12:10:18] SGroup 1 is invalid and will be ignored +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20531,7 +20580,7 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20540,9 +20589,9 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] multiple bonds with same bookmark -67: [03:04:12] SGroup 2 is invalid and will be ignored -67: [03:04:12] +67: [12:10:18] multiple bonds with same bookmark +67: [12:10:18] SGroup 2 is invalid and will be ignored +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20551,7 +20600,7 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20560,63 +20609,24 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [03:04:12] multiple atoms with same bookmark -67: [03:04:12] SGroup 2 is invalid and will be ignored -69: =============================================================================== -69: All tests passed (100 assertions in 2 test cases) -69: - 56/208 Test #69: XYZFileParserCatchTest ................. Passed 0.08 sec -test 71 - Start 71: testSubstructMatch - -71: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -71: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -71: Test timeout computed to be: 1500 -67: [03:04:12] Explicit valence for atom # 2 O, 3, is greater than permitted -67: [03:04:12] Explicit valence for atom # 1 O, 3, is greater than permitted -67: [03:04:12] Explicit valence for atom # 1 C, 5, is greater than permitted -59: [03:04:12] Finished: testForwardSDSupplier() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testMissingCRSDSupplier() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testIssue3482695() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- - 57/208 Test #62: testMolWriter .......................... Passed 0.43 sec -test 72 - Start 72: substructTestCatch - -72: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -72: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct -72: Test timeout computed to be: 1500 -59: [03:04:12] ERROR: Cannot convert 'foo' to unsigned int on line 557 -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] Finished: testIssue3525673() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testBlankLinesInProps() -59: [03:04:12] ----------------------------------------- +67: [12:10:18] multiple atoms with same bookmark +67: [12:10:18] SGroup 2 is invalid and will be ignored +3: static RDAny:0.062175 s +67: [12:10:18] Explicit valence for atom # 2 O, 3, is greater than permitted +67: [12:10:18] Explicit valence for atom # 1 O, 3, is greater than permitted +67: [12:10:18] Explicit valence for atom # 1 C, 5, is greater than permitted +59: [12:10:18] Finished: testForwardSDSupplier() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testSkipLines() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testMissingCRSDSupplier() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testGitHub23() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testIssue3482695() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testGitHub88() -59: [03:04:12] ----------------------------------------- -59: -59: [03:04:12] ----------------------------------------- -67: [03:04:12] sanitise [03:04:12] UNK: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero +59: [12:10:18] ----------------------------------------- 71: ----------------- Test 1 71: Done 71: @@ -20641,43 +20651,76 @@ 71: ----------------- Testing serial numbers on recursive queries 71: Done 71: -71: [03:04:12] ------------------------------------- -71: [03:04:12] Test multithreading +71: [12:10:18] ------------------------------------- +71: [12:10:18] Test multithreading 71: reading molecules -59: [03:04:12] Finished: testGitHub2285() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] ERROR: Cannot convert 'foo' to unsigned int on line 557 +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Finished: testIssue3525673() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testBlankLinesInProps() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -59: [03:04:12] ERROR: Smiles parse error on line 1 -59: [03:04:12] ERROR: Cannot create molecule from : 'c1ccccc' -59: [03:04:12] SMILES Parse Error: extra open parentheses for input: 'C(C' -59: [03:04:12] ERROR: Smiles parse error on line 3 -59: [03:04:12] ERROR: Cannot create molecule from : 'C(C' -59: [03:04:12] Explicit valence for atom # 1 C, 5, is greater than permitted -59: [03:04:12] ERROR: Could not sanitize molecule on line 5 -59: [03:04:12] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -59: [03:04:12] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [03:04:12] ERROR: Could not sanitize molecule ending on line 21 -59: [03:04:12] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [03:04:12] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [03:04:12] ERROR: Could not sanitize molecule ending on line 21 -59: [03:04:12] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [03:04:12] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [03:04:12] ERROR: Could not sanitize molecule ending on line 21 -59: [03:04:12] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [03:04:12] ERROR: Atom line too short: ' -9.6' on line 28 -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [03:04:12] ERROR: Could not sanitize molecule ending on line 21 -59: [03:04:12] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [03:04:12] ERROR: Atom line too short: ' -9.6' on line 28 -59: [03:04:12] ERROR: moving to the beginning of the next molecule -59: [03:04:12] Finished: testGitHub2479() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testSkipLines() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testGitHub23() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testGitHub88() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +69: =============================================================================== +69: All tests passed (100 assertions in 2 test cases) +69: +67: [12:10:18] sanitise [12:10:18] UNK: [12:10:18] Warning: molecule is tagged as 3D, but all Z coords are zero + 56/208 Test #69: XYZFileParserCatchTest ................. Passed 0.13 sec +test 72 + Start 72: substructTestCatch + +72: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +72: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Substruct +72: Test timeout computed to be: 1500 +59: [12:10:18] Finished: testGitHub2285() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +59: [12:10:18] ERROR: Smiles parse error on line 1 +59: [12:10:18] ERROR: Cannot create molecule from : 'c1ccccc' +59: [12:10:18] SMILES Parse Error: extra open parentheses for input: 'C(C' +59: [12:10:18] ERROR: Smiles parse error on line 3 +59: [12:10:18] ERROR: Cannot create molecule from : 'C(C' +59: [12:10:18] Explicit valence for atom # 1 C, 5, is greater than permitted +59: [12:10:18] ERROR: Could not sanitize molecule on line 5 +59: [12:10:18] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +59: [12:10:18] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [12:10:18] ERROR: Could not sanitize molecule ending on line 21 +59: [12:10:18] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [12:10:18] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [12:10:18] ERROR: Could not sanitize molecule ending on line 21 +59: [12:10:18] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [12:10:18] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [12:10:18] ERROR: Could not sanitize molecule ending on line 21 +59: [12:10:18] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [12:10:18] ERROR: Atom line too short: ' -9.6' on line 28 +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [12:10:18] ERROR: Could not sanitize molecule ending on line 21 +59: [12:10:18] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [12:10:18] ERROR: Atom line too short: ' -9.6' on line 28 +59: [12:10:18] ERROR: moving to the beginning of the next molecule +59: [12:10:18] Finished: testGitHub2479() +59: [12:10:18] ----------------------------------------- +59: +59: [12:10:18] ----------------------------------------- +59: [12:10:18] 59: 59: **** 59: Invariant Violation @@ -20686,15 +20729,15 @@ 59: Failed Expression: bnd 59: **** 59: -59: [03:04:12] Finished: testGitHub2881() -59: [03:04:12] ----------------------------------------- +67: [12:10:18] skipping block at line 7: 'BEGIN ATOM' +59: [12:10:18] Finished: testGitHub2881() +59: [12:10:18] ----------------------------------------- 59: -59: [03:04:12] ----------------------------------------- -59: [03:04:12] Finished: testGitHub3517() -59: [03:04:12] ----------------------------------------- +59: [12:10:18] ----------------------------------------- +59: [12:10:18] Finished: testGitHub3517() +59: [12:10:18] ----------------------------------------- 59: -67: [03:04:12] skipping block at line 7: 'BEGIN ATOM' -67: [03:04:12] +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20703,7 +20746,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [03:04:12] +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20712,7 +20755,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [03:04:12] +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20721,7 +20764,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [03:04:12] +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20730,7 +20773,20 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [03:04:12] +71: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +71: processing +71: launch :0 +71: launch :1 +71: launch :2 +71: launch :3 + 57/208 Test #59: testMolSupplier ........................ Passed 0.75 sec +test 73 + Start 73: testGenericGroups + +73: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +73: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups +73: Test timeout computed to be: 1500 +67: [12:10:18] 67: 67: **** 67: Pre-condition Violation @@ -20739,9 +20795,9 @@ 67: Failed Expression: dp_sInStream != nullptr 67: **** 67: -67: [03:04:12] Found a SCD/SED line with missing/empty SDT specification at line 21 -67: [03:04:12] Found a SCD/SED line with missing/empty SDT specification at line 20 -67: [03:04:12] +67: [12:10:18] Found a SCD/SED line with missing/empty SDT specification at line 21 +67: [12:10:18] Found a SCD/SED line with missing/empty SDT specification at line 20 +67: [12:10:18] 67: 67: **** 67: Post-condition Violation @@ -20750,20 +20806,13 @@ 67: Failed Expression: anum > -1 67: **** 67: -67: [03:04:12] BEGIN SGROUP line not found on line 14 -67: [03:04:12] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -67: [03:04:12] END SGROUP line not found on line 14 -67: [03:04:12] END SGROUP line not found on line 14 - 58/208 Test #59: testMolSupplier ........................ Passed 0.62 sec -test 73 - Start 73: testGenericGroups - -73: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -73: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/GenericGroups -73: Test timeout computed to be: 1500 -67: [03:04:12] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -67: [03:04:12] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -67: [03:04:12] +67: [12:10:18] BEGIN SGROUP line not found on line 14 +67: [12:10:18] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +67: [12:10:18] END SGROUP line not found on line 14 +67: [12:10:18] END SGROUP line not found on line 14 +67: [12:10:18] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +67: [12:10:18] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +67: [12:10:18] 67: 67: **** 67: Range Error @@ -20772,301 +20821,260 @@ 67: Failed Expression: 99 < 9 67: **** 67: -67: [03:04:12] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -67: [03:04:12] Multiple ATTCHPT values for atom 2 on line 9 -67: [03:04:12] Found a SCD/SED line with missing/empty SDT specification at line 12 -67: [03:04:12] SMARTS Parse Error: syntax error while parsing: [#6;R -67: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -67: [03:04:12] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -67: [03:04:12] Skipping empty SMARTS value for SMARTSQ. -67: [03:04:12] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -67: [03:04:12] Found a SCD/SED line with missing/empty SDT specification at line 12 -67: [03:04:12] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -70: [03:04:12] Invalid or missing fragment id from CDXML fragment, assigning new one... -70: [03:04:12] Explicit valence for atom # 3 N, 4, is greater than permitted -70: [03:04:12] CDXMLParser: failed sanitizing skipping fragment 32 -70: [03:04:12] Bad bond in CDXML skipping fragment 58... -70: [03:04:12] Invalid or missing fragment id from CDXML fragment, assigning new one... -70: [03:04:12] Bad bond in CDXML skipping fragment 58... -67: [03:04:12] Warning: molecule is tagged as 3D, but all Z coords are zero +67: [12:10:18] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +67: [12:10:18] Multiple ATTCHPT values for atom 2 on line 9 +67: [12:10:18] Found a SCD/SED line with missing/empty SDT specification at line 12 +67: [12:10:18] SMARTS Parse Error: syntax error while parsing: [#6;R +67: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +67: [12:10:18] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +67: [12:10:18] Skipping empty SMARTS value for SMARTSQ. +67: [12:10:18] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +67: [12:10:18] Found a SCD/SED line with missing/empty SDT specification at line 12 +67: [12:10:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +70: [12:10:18] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [12:10:18] Explicit valence for atom # 3 N, 4, is greater than permitted +70: [12:10:18] CDXMLParser: failed sanitizing skipping fragment 32 +70: [12:10:18] Bad bond in CDXML skipping fragment 58... +70: [12:10:18] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [12:10:18] Bad bond in CDXML skipping fragment 58... +67: [12:10:18] Warning: molecule is tagged as 3D, but all Z coords are zero 67: =============================================================================== 67: All tests passed (778 assertions in 67 test cases) 67: - 59/208 Test #67: fileParsersCatchTest ................... Passed 0.23 sec + 58/208 Test #67: fileParsersCatchTest ................... Passed 0.25 sec test 74 Start 74: testReaction 74: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 74: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 74: Test timeout computed to be: 1500 -71: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -71: processing -71: launch :0 -71: launch :1 -71: launch :2 -71: launch :3 -73: =============================================================================== -73: All tests passed (490 assertions in 18 test cases) -73: +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors 74: smi: O=C1CNC(=O)CN1 74: 1: O=C1CNC(=O)CN1 74: 2: COOC -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -74: [03:04:12] 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: [12:10:18] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +74: [12:10:18] 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 - 60/208 Test #73: testGenericGroups ...................... Passed 0.11 sec +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 4 +73: =============================================================================== +73: All tests passed (490 assertions in 18 test cases) +73: + 59/208 Test #73: testGenericGroups ...................... Passed 0.18 sec test 75 Start 75: testReactionFingerprints 75: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 75: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 75: Test timeout computed to be: 1500 -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 4 -51: ....E..... -51: ====================================================================== -51: ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) -51: ---------------------------------------------------------------------- -51: Traceback (most recent call last): -51: File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D -51: dmat3D = getDistMat(mol) -51: ^^^^^^^^^^^^^^^ -51: File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 31, in getDistMat -51: res = np.zeros(nl, np.float) -51: ^^^^^^^^ -51: File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ -51: raise AttributeError(__former_attrs__[attr]) -51: AttributeError: module 'numpy' has no attribute 'float'. -51: `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. -51: The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: -51: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations -51: -51: ---------------------------------------------------------------------- -51: Ran 10 tests in 0.431s -51: -51: FAILED (errors=1) -74: [03:04:12] atom 0 in product 0 has multiple charge specifications. -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] WARNING: not removing hydrogen atom without neighbors +70: [12:10:18] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. +74: [12:10:18] atom 0 in product 0 has multiple charge specifications. 74: mass: 15.0001 74: Oc1ccccn1 74: Oc1ccc[nH]1 -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -75: [03:04:12] ------------------------------------- -75: [03:04:12] Test Reaction StructuralFingerprint -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -70: [03:04:12] WARNING: not removing hydrogen atom without neighbors -70: [03:04:12] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -74: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: ([C:2] -74: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -74: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: [C:2]) -74: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -75: [03:04:12] ------------------------------------- -75: [03:04:12] Test Reaction DifferenceFingerprint - 61/208 Test #75: testReactionFingerprints ............... Passed 0.06 sec -test 76 - Start 76: testEnumeration - -76: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -76: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions -76: Test timeout computed to be: 1500 -74: [03:04:12] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -74: [03:04:12] 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: [03:04:12] reactant 2 has no mapped atoms. -74: [03:04:12] >> Atoms within one molecule have different RXN roles. -74: [03:04:12] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -74: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: ([C:2] -74: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -74: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -74: [03:04:12] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -74: [03:04:12] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -74: [03:04:12] reactant 0 has no mapped atoms. -74: [03:04:12] reactant 1 has no mapped atoms. -74: [03:04:12] reactant 3 has no mapped atoms. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 5 found multiple times. -74: [03:04:12] product atom-mapping number 6 found multiple times. -74: [03:04:12] product atom-mapping number 7 found multiple times. -74: [03:04:12] product atom-mapping number 8 found multiple times. -74: [03:04:12] product atom-mapping number 12 found multiple times. -74: [03:04:12] product atom-mapping number 9 found multiple times. -74: [03:04:12] product atom-mapping number 10 found multiple times. -74: [03:04:12] product atom-mapping number 11 found multiple times. -74: [03:04:12] reactant 0 has no mapped atoms. -74: [03:04:12] reactant 1 has no mapped atoms. -74: [03:04:12] reactant 3 has no mapped atoms. -74: [03:04:12] reactant atom-mapping number 19 found multiple times. -74: [03:04:12] reactant atom-mapping number 25 found multiple times. -74: [03:04:12] reactant atom-mapping number 20 found multiple times. -74: [03:04:12] reactant atom-mapping number 21 found multiple times. -74: [03:04:12] reactant atom-mapping number 22 found multiple times. -74: [03:04:12] reactant atom-mapping number 23 found multiple times. -74: [03:04:12] reactant atom-mapping number 24 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. +74: [12:10:18] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +74: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +74: [12:10:18] SMARTS Parse Error: syntax error while parsing: ([C:2] +74: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +74: [12:10:18] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +74: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +74: [12:10:18] SMARTS Parse Error: syntax error while parsing: [C:2]) +74: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +74: [12:10:18] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +74: [12:10:18] 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: [12:10:18] reactant 2 has no mapped atoms. +74: [12:10:18] >> Atoms within one molecule have different RXN roles. +74: [12:10:18] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +74: [12:10:18] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +74: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +74: [12:10:18] SMARTS Parse Error: syntax error while parsing: ([C:2] +74: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +74: [12:10:18] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +74: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +74: [12:10:18] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +74: [12:10:18] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +74: [12:10:18] reactant 0 has no mapped atoms. +74: [12:10:18] reactant 1 has no mapped atoms. +74: [12:10:18] reactant 3 has no mapped atoms. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +75: [12:10:18] ------------------------------------- +75: [12:10:18] Test Reaction StructuralFingerprint +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 5 found multiple times. +74: [12:10:18] product atom-mapping number 6 found multiple times. +74: [12:10:18] product atom-mapping number 7 found multiple times. +74: [12:10:18] product atom-mapping number 8 found multiple times. +74: [12:10:18] product atom-mapping number 12 found multiple times. +74: [12:10:18] product atom-mapping number 9 found multiple times. +74: [12:10:18] product atom-mapping number 10 found multiple times. +74: [12:10:18] product atom-mapping number 11 found multiple times. +74: [12:10:18] reactant 0 has no mapped atoms. +74: [12:10:18] reactant 1 has no mapped atoms. +74: [12:10:18] reactant 3 has no mapped atoms. +74: [12:10:18] reactant atom-mapping number 19 found multiple times. +74: [12:10:18] reactant atom-mapping number 25 found multiple times. +74: [12:10:18] reactant atom-mapping number 20 found multiple times. +74: [12:10:18] reactant atom-mapping number 21 found multiple times. +74: [12:10:18] reactant atom-mapping number 22 found multiple times. +74: [12:10:18] reactant atom-mapping number 23 found multiple times. +74: [12:10:18] reactant atom-mapping number 24 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. 74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. 74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [03:04:12] product atom-mapping number 5 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 5 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 5 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 5 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. +70: [12:10:18] Incomplete atom labelling, cannot make bond +70: [12:10:18] Incomplete atom labelling, cannot make bond 74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [03:04:12] product atom-mapping number 5 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 5 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 5 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 5 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. 74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. 74: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. 74: F[C@](Cl)(Br)O[C@](F)(Cl)Br -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 4 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] mapped atoms in the reactants were not mapped in the products. +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 4 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 4 -74: [03:04:12] product atom-mapping number 3 found multiple times. -74: [03:04:12] product atom-mapping number 2 found multiple times. -74: [03:04:12] product atom-mapping number 1 found multiple times. -74: [03:04:12] mapped atoms in the reactants were not mapped in the products. +74: [12:10:18] product atom-mapping number 3 found multiple times. +74: [12:10:18] product atom-mapping number 2 found multiple times. +74: [12:10:18] product atom-mapping number 1 found multiple times. +74: [12:10:18] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 4 -74: [03:04:12] product atom-mapping number 6 not found in reactants. -74: [03:04:12] product atom-mapping number 7 not found in reactants. -74: [03:04:12] product atom-mapping number 8 not found in reactants. -74: [03:04:12] product atom-mapping number 7 not found in reactants. -74: [03:04:12] product atom-mapping number 8 not found in reactants. -74: [03:04:12] product atom-mapping number 9 not found in reactants. -74: [03:04:12] product atom-mapping number 10 not found in reactants. -74: [03:04:12] mapped atoms in the reactants were not mapped in the products. +74: [12:10:18] product atom-mapping number 6 not found in reactants. +74: [12:10:18] product atom-mapping number 7 not found in reactants. +74: [12:10:18] product atom-mapping number 8 not found in reactants. +74: [12:10:18] product atom-mapping number 7 not found in reactants. +74: [12:10:18] product atom-mapping number 8 not found in reactants. +74: [12:10:18] product atom-mapping number 9 not found in reactants. +74: [12:10:18] product atom-mapping number 10 not found in reactants. +74: [12:10:18] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 6 -74: [03:04:12] product atom-mapping number 7 not found in reactants. -74: [03:04:12] product atom-mapping number 8 not found in reactants. -74: [03:04:12] product atom-mapping number 9 not found in reactants. -74: [03:04:12] product atom-mapping number 10 not found in reactants. -74: [03:04:12] mapped atoms in the reactants were not mapped in the products. +74: [12:10:18] product atom-mapping number 7 not found in reactants. +74: [12:10:18] product atom-mapping number 8 not found in reactants. +74: [12:10:18] product atom-mapping number 9 not found in reactants. +74: [12:10:18] product atom-mapping number 10 not found in reactants. +74: [12:10:18] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 6 +62: [12:10:18] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [12:10:18] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [12:10:18] Warning: molecule is tagged as 3D, but all Z coords are zero 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] - 62/208 Test #51: pyDepictor .............................***Failed 1.12 sec -....E..... -====================================================================== -ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D - dmat3D = getDistMat(mol) - ^^^^^^^^^^^^^^^ - File "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 31, in getDistMat - res = np.zeros(nl, np.float) - ^^^^^^^^ - File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 305, in __getattr__ - raise AttributeError(__former_attrs__[attr]) -AttributeError: module 'numpy' has no attribute 'float'. -`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 - ----------------------------------------------------------------------- -Ran 10 tests in 0.431s - -FAILED (errors=1) +70: [12:10:18] Incomplete atom labelling, cannot make bond +75: [12:10:18] ------------------------------------- +75: [12:10:18] Test Reaction DifferenceFingerprint +62: [12:10:18] bond with order 0 found on line 11. This is not part of the MDL specification. +62: [12:10:18] bond with order 0 found on line 16. This is not part of the MDL specification. + 60/208 Test #75: testReactionFingerprints ............... Passed 0.12 sec +test 76 + Start 76: testEnumeration +76: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +76: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions +76: Test timeout computed to be: 1500 +70: [12:10:18] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [12:10:18] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [12:10:18] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +70: [12:10:18] Failed to parse XML fragment 5 node: b attribute: Order: 5 +70: [12:10:18] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [12:10:18] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [12:10:18] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +70: [12:10:18] Failed to parse XML fragment 5 node: b attribute: Order: 5 +70: =============================================================================== +70: All tests passed (200 assertions in 1 test case) +70: + 61/208 Test #70: cdxmlParserCatchTest ................... Passed 0.46 sec test 77 Start 77: rxnTestCatch 77: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 77: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemReactions 77: Test timeout computed to be: 1500 -74: [03:04:12] 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: [03:04:12] product atom-mapping number 17 not found in reactants. -74: [03:04:12] product atom-mapping number 18 not found in reactants. -74: [03:04:12] mapped atoms in the reactants were not mapped in the products. -74: unmapped numbers are: 12 -70: [03:04:12] Incomplete atom labelling, cannot make bond -70: [03:04:12] Incomplete atom labelling, cannot make bond -72: =============================================================================== -72: All tests passed (91 assertions in 5 test cases) -72: - 63/208 Test #72: substructTestCatch ..................... Passed 0.33 sec + 62/208 Test #62: testMolWriter .......................... Passed 0.77 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-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 78: Test timeout computed to be: 1500 -70: [03:04:12] Incomplete atom labelling, cannot make bond +77: [12:10:18] atom 0 in product 0 has multiple charge specifications. +74: [12:10:18] 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 71: done 71: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 71: processing2 @@ -21074,18 +21082,23 @@ 71: launch2 :1 71: launch2 :2 71: launch2 :3 -70: [03:04:12] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [03:04:12] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [03:04:12] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -70: [03:04:12] Failed to parse XML fragment 5 node: b attribute: Order: 5 -70: [03:04:12] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [03:04:13] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [03:04:13] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -70: [03:04:13] Failed to parse XML fragment 5 node: b attribute: Order: 5 -70: =============================================================================== -70: All tests passed (200 assertions in 1 test case) -70: - 64/208 Test #70: cdxmlParserCatchTest ................... Passed 0.45 sec +77: [12:10:18] mapped atoms in the reactants were not mapped in the products. +77: unmapped numbers are: 2 +77: [12:10:18] mapped atoms in the reactants were not mapped in the products. +77: unmapped numbers are: 2 +77: [12:10:18] SMARTS Parse Error: unclosed ring for input: 'CC1' +77: [12:10:18] SMILES Parse Error: unclosed ring for input: 'CC1' +77: [12:10:18] mapped atoms in the reactants were not mapped in the products. +77: unmapped numbers are: 2 +77: [12:10:18] product atom-mapping number 2 not found in reactants. +77: [12:10:18] mapped atoms in the reactants were not mapped in the products. +77: unmapped numbers are: 2 +77: [12:10:18] product atom-mapping number 2 not found in reactants. +77: [12:10:18] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +77: =============================================================================== +77: All tests passed (450 assertions in 14 test cases) +77: + 63/208 Test #77: rxnTestCatch ........................... Passed 0.12 sec test 79 Start 79: pyChemReactionEnumerations @@ -21100,51 +21113,94 @@ 71: launch3 :1 71: launch3 :2 71: launch3 :3 -77: [03:04:13] atom 0 in product 0 has multiple charge specifications. +74: [12:10:18] product atom-mapping number 17 not found in reactants. +74: [12:10:18] product atom-mapping number 18 not found in reactants. +74: [12:10:18] mapped atoms in the reactants were not mapped in the products. +74: unmapped numbers are: 12 76: 30000000 30000000 -77: [03:04:13] mapped atoms in the reactants were not mapped in the products. -77: unmapped numbers are: 2 -77: [03:04:13] mapped atoms in the reactants were not mapped in the products. -77: unmapped numbers are: 2 -77: [03:04:13] SMARTS Parse Error: unclosed ring for input: 'CC1' -77: [03:04:13] SMILES Parse Error: unclosed ring for input: 'CC1' -77: [03:04:13] mapped atoms in the reactants were not mapped in the products. -77: unmapped numbers are: 2 -77: [03:04:13] product atom-mapping number 2 not found in reactants. -77: [03:04:13] mapped atoms in the reactants were not mapped in the products. -77: unmapped numbers are: 2 -77: [03:04:13] product atom-mapping number 2 not found in reactants. -77: [03:04:13] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -77: =============================================================================== -77: All tests passed (450 assertions in 14 test cases) -77: -32: [03:04:13] Maximum BFS search size exceeded. +71: done +71: [12:10:18] done +71: [12:10:18] ------------------------------------- +71: [12:10:18] Test GitHub issue 15 +71: [12:10:18] done +71: [12:10:18] ------------------------------------- +71: [12:10:18] Test GitHub issue 409 +71: [12:10:18] done +71: [12:10:18] ------------------------------------- +71: [12:10:18] Test chiral matching +71: [12:10:18] done +71: [12:10:18] ------------------------------------- +71: [12:10:18] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +71: [12:10:18] done +71: [12:10:18] ------------------------------------- +71: [12:10:18] Test dative-bond matching +71: [12:10:18] done +71: [12:10:18] ------------------------------------- +71: [12:10:18] Test cis/trans matching +71: [12:10:18] done +71: [12:10:18] ------------------------------------- +71: [12:10:18] Test cis/trans matching part 2 +74: [12:10:18] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +74: [12:10:18] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +74: +71: [12:10:18] done +71: [12:10:18] ------------------------------------- +71: [12:10:18] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +71: [12:10:18] done +74: [12:10:18] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +71: [12:10:18] ------------------------------------- +71: [12:10:18] Testing matching E/Z against Cis/Trans stereo bonds +71: [12:10:18] +71: +71: **** +71: Pre-condition Violation +71: matches must not be empty +71: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +71: Failed Expression: !matches.empty() +71: **** +71: +71: [12:10:18] +71: +71: **** +71: Pre-condition Violation +71: matches must not be empty +71: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +71: Failed Expression: !matches.empty() +71: **** +71: +74: ------------- +74: CCOc1ccccc1 +32: [12:10:18] Maximum BFS search size exceeded. 32: This is likely due to a highly symmetric fused ring system. - 65/208 Test #77: rxnTestCatch ........................... Passed 0.19 sec + 64/208 Test #71: testSubstructMatch ..................... Passed 0.85 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-x86_64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 80: Test timeout computed to be: 1500 -74: [03:04:13] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -74: [03:04:13] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -74: -74: [03:04:13] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -74: ------------- -74: CCOc1ccccc1 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 - 66/208 Test #32: graphmolMolOpsTest ..................... Passed 1.92 sec +72: =============================================================================== +72: All tests passed (91 assertions in 5 test cases) +72: + 65/208 Test #72: substructTestCatch ..................... Passed 0.89 sec test 81 Start 81: testChemTransforms 81: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 81: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms 81: Test timeout computed to be: 1500 + 66/208 Test #32: graphmolMolOpsTest ..................... Passed 2.74 sec +test 82 + Start 82: chemTransformsTestCatch + +82: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch +82: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms +82: Test timeout computed to be: 1500 81: 1 smi: CC 81: 1 smi: CC 81: 2 smi: CCO[C@H](N)P @@ -21153,73 +21209,10 @@ 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 -71: done -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Test GitHub issue 15 -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Test GitHub issue 409 -81: [03:04:13] SMARTS Parse Error: syntax error while parsing: bar -81: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Test chiral matching -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Test dative-bond matching -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Test cis/trans matching -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Test cis/trans matching part 2 -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -71: [03:04:13] done -71: [03:04:13] ------------------------------------- -71: [03:04:13] Testing matching E/Z against Cis/Trans stereo bonds -71: [03:04:13] -71: -71: **** -71: Pre-condition Violation -71: matches must not be empty -71: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -71: Failed Expression: !matches.empty() -71: **** -71: -71: [03:04:13] -71: -71: **** -71: Pre-condition Violation -71: matches must not be empty -71: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -71: Failed Expression: !matches.empty() -71: **** -71: - 67/208 Test #71: testSubstructMatch ..................... Passed 0.69 sec -test 82 - Start 82: chemTransformsTestCatch - -82: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch -82: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ChemTransforms -82: Test timeout computed to be: 1500 - 68/208 Test #81: testChemTransforms ..................... Passed 0.24 sec -test 83 - Start 83: tautomerQueryTestCatch - -83: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -83: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery -83: Test timeout computed to be: 1500 -74: [03:04:13] reactant 0 has no mapped atoms. -74: [03:04:13] product 0 has no mapped atoms. -74: [03:04:13] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. -82: [03:04:13] Incomplete atom labelling, cannot make bond -82: [03:04:13] +81: [12:10:19] SMARTS Parse Error: syntax error while parsing: bar +81: [12:10:19] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +82: [12:10:19] Incomplete atom labelling, cannot make bond +82: [12:10:19] 82: 82: **** 82: Invariant Violation @@ -21228,15 +21221,55 @@ 82: Failed Expression: !bond.b 82: **** 82: - 69/208 Test #74: testReaction ........................... Passed 0.72 sec -test 84 - Start 84: pyTautomerQuery - -84: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -84: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -84: Test timeout computed to be: 1500 -82: [03:04:13] Incomplete atom labelling, cannot make bond -82: [03:04:13] +82: [12:10:19] Incomplete atom labelling, cannot make bond +82: [12:10:19] +82: +82: **** +82: Invariant Violation +82: molzip: bond info already exists for end atom with label:1 +82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: !bond.b +82: **** +82: +82: [12:10:19] Incomplete atom labelling, cannot make bond +82: [12:10:19] +82: +82: **** +82: Invariant Violation +82: molzip: bond info already exists for end atom with label:1 +82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: !bond.b +82: **** +82: +58: [12:10:19] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [12:10:19] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [12:10:19] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [12:10:19] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [12:10:19] 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: [12:10:19] +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: +82: [12:10:19] Incomplete atom labelling, cannot make bond +82: [12:10:19] Incomplete atom labelling, cannot make bond +82: [12:10:19] Incomplete atom labelling, cannot make bond +82: [12:10:19] +82: +82: **** +82: Invariant Violation +82: molzip: bond info already exists for end atom with label:1 +82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: !bond.b +82: **** +82: +82: [12:10:19] Incomplete atom labelling, cannot make bond +82: [12:10:19] 82: 82: **** 82: Invariant Violation @@ -21245,7 +21278,126 @@ 82: Failed Expression: !bond.b 82: **** 82: -78: [03:04:13] +82: [12:10:19] +82: +82: **** +82: Invariant Violation +82: molzip: zipped Bond already exists, perhaps labels are duplicated +82: Violation occurred on line 738 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp +82: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) +82: **** +82: +82: =============================================================================== +82: All tests passed (531 assertions in 4 test cases) +82: + 67/208 Test #82: chemTransformsTestCatch ................ Passed 0.20 sec +test 83 + Start 83: tautomerQueryTestCatch + +83: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +83: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery +83: Test timeout computed to be: 1500 + 68/208 Test #81: testChemTransforms ..................... Passed 0.27 sec +test 84 + Start 84: pyTautomerQuery + +84: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +84: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +84: Test timeout computed to be: 1500 +3: dynamic RDAny:0.460414 s +3: static RDValue:1e-06 s +74: [12:10:19] reactant 0 has no mapped atoms. +74: [12:10:19] product 0 has no mapped atoms. +74: [12:10:19] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 69/208 Test #74: testReaction ........................... Passed 1.25 sec +test 85 + Start 85: testSubgraphs1 + +85: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +85: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +85: Test timeout computed to be: 1500 +79: [12:10:19] == testCartesianProduct +83: =============================================================================== +83: All tests passed (86 assertions in 12 test cases) +83: +85: ----------------------- +85: Subgraph retrieval +85: Finished +85: ----------------------- +85: testSubgraphs2a + 70/208 Test #83: tautomerQueryTestCatch ................. Passed 0.25 sec +test 86 + Start 86: testSubgraphs2 + +86: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 +86: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs +86: Test timeout computed to be: 1500 +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) +85: Finished +85: ----------------------- +85: testSubgraphs2 +3: dynamic RDValue:0.056401 s +3: deleted! +3: [12:10:19] ------------------------------------- +3: [12:10:19] Testing String Pickle Roundtrips. +3: [12:10:19] done +3: [12:10:19] ------------------------------------- +3: [12:10:19] Testing conversion of vect to string. +3: [12:10:19] done +3: [12:10:19] ------------------------------------- +3: [12:10:19] Testing returning const references. +3: [12:10:19] any cast +3: [12:10:19] done: 0.001705 300000 +3: [12:10:19] copy +86: ----------------------- +86: Test1: pathToSubmol +3: [12:10:19] done: 0.001731 300000 +3: [12:10:19] ref +3: [12:10:19] done: 0.001624 300000 +3: [12:10:19] dict +79: .[12:10:19] == testEnumerateLibrary +86: Finished +86: ----------------------- +86: Test2: Atom Environments +86: Finished +86: ----------------------- +86: Test 3: Atom Environments (Extension) +86: Finished +86: ----------------------- +86: Testing github Issue103: stereochemistry and pathToSubmol +86: Finished +86: ----------------------- +86: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) +86: Finished +3: [12:10:19] done: 0.006147 300000 +3: [12:10:19] ref with hasVal +3: [12:10:19] done: 0.00264 300000 +3: [12:10:19] done +3: [12:10:19] ------------------------------------- +3: [12:10:19] Testing dict update. +3: [12:10:19] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! + 71/208 Test #3: testDict ............................... Passed 3.89 sec +test 87 + Start 87: filterCatalogTest + +87: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +87: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog +87: Test timeout computed to be: 1500 + 72/208 Test #86: testSubgraphs2 ......................... Passed 0.08 sec +test 88 + Start 88: pyFilterCatalog + +88: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +88: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +88: Test timeout computed to be: 1500 +78: [12:10:19] 78: 78: **** 78: Pre-condition Violation @@ -21254,7 +21406,7 @@ 78: Failed Expression: d_implicitValence > -1 78: **** 78: -78: [03:04:13] +78: [12:10:19] 78: 78: **** 78: Pre-condition Violation @@ -21263,83 +21415,204 @@ 78: Failed Expression: d_implicitValence > -1 78: **** 78: -78: ...[03:04:13] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [03:04:13] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [03:04:13] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [03:04:13] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: .[03:04:13] product atom-mapping number 1 found multiple times. -78: [03:04:13] product atom-mapping number 1 found multiple times. -82: [03:04:13] Incomplete atom labelling, cannot make bond -82: [03:04:13] -82: -82: **** -82: Invariant Violation -82: molzip: bond info already exists for end atom with label:1 -82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: !bond.b -82: **** -82: -78: ................[03:04:13] mapped atoms in the reactants were not mapped in the products. +78: ...[12:10:19] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [12:10:19] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [12:10:19] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [12:10:19] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: .[12:10:19] product atom-mapping number 1 found multiple times. +78: [12:10:19] product atom-mapping number 1 found multiple times. +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 +78: ................[12:10:19] mapped atoms in the reactants were not mapped in the products. +78: unmapped numbers are: 3 +78: [12:10:19] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -80: .[03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -78: [03:04:13] mapped atoms in the reactants were not mapped in the products. +78: .[12:10:19] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. +78: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:515: DeprecationWarning: Please use assertTrue instead. +78: self.failUnless(rxn) +78: [12:10:19] reactant 2 has no mapped atoms. +78: [12:10:19] reactant 2 has no mapped atoms. +78: [12:10:19] 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: ......[12:10:19] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +78: [12:10:19] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +78: [12:10:19] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +78: [12:10:19] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +78: .[12:10:19] reactant atom-mapping number 1 found multiple times. +78: [12:10:19] product atom-mapping number 2 not found in reactants. +78: [12:10:19] mapped atoms in the reactants were not mapped in the products. +78: unmapped numbers are: 4 +78: [12:10:19] product atom-mapping number 5 not found in reactants. +79: ..[12:10:19] == testRGroupState +79: .[12:10:19] == testRandomEnumerateAllBBsLibrary +79: ** [1, 1] +79: ** [0, 2] +79: ** [1, 0] +85: Finished +85: ----------------------- +85: Path retrieval +85: Finished +85: ----------------------- +85: Path retrieval2 +85: Finished +85: ----------------------- +85: Unique Subgraph retrieval +85: Finished +85: ----------------------- +85: testUniqueSubgraphs2 +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 +79: .[12:10:19] == testRandomEnumerateLibrary +87: Warning: molecule failed filter +87: Warning: molecule failed filter: reason hzone_phenol_A(479) +87: v = { +87: 0,23}, +87: 1,22}, +87: 2,20}, +87: 3,19}, +87: 4,25}, +87: 5,24}, +87: 6,18}, +87: 7,17}, +87: 8,16}, +87: 9,21}, +87: } +87: match = { +87: 0,23}, +87: 1,22}, +87: 2,20}, +87: 3,19}, +87: 4,25}, +87: 5,24}, +87: 6,18}, +87: 7,17}, +87: 8,16}, +87: 9,21}, +87: } +87: Warning: molecule failed filter +87: Warning: molecule failed filter: reason cyano_imine_B(17) +87: v = { +87: 0,11}, +87: 1,12}, +87: 2,13}, +87: 3,14}, +87: 4,15}, +87: 5,10}, +87: 6,9}, +87: 7,8}, +87: 8,7}, +87: 9,6}, +87: 10,5}, +87: 11,17}, +87: 12,16}, +87: } +87: match = { +87: 0,11}, +87: 1,12}, +87: 2,13}, +87: 3,14}, +87: 4,15}, +87: 5,10}, +87: 6,9}, +87: 7,8}, +87: 8,7}, +87: 9,6}, +87: 10,5}, +87: 11,17}, +87: 12,16}, +87: } +87: Warning: molecule failed filter +87: Warning: molecule failed filter: reason keto_keto_gamma(5) +87: v = { +87: 0,0}, +87: 1,1}, +87: 2,2}, +87: 3,4}, +87: 4,5}, +87: 5,6}, +87: 6,7}, +87: 7,8}, +87: 8,9}, +87: 9,14}, +87: 10,15}, +87: 11,16}, +87: } +87: match = { +87: 0,0}, +87: 1,1}, +87: 2,2}, +87: 3,4}, +87: 4,5}, +87: 5,6}, +87: 6,7}, +87: 7,8}, +87: 8,9}, +87: 9,14}, +87: 10,15}, +87: 11,16}, +87: } +79: .[12:10:19] == testRandomSample +80: .[12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] 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: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -78: .[03:04:13] mapped atoms in the reactants were not mapped in the products. -78: unmapped numbers are: 3 -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] reactant 0 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] product 0 has no mapped atoms. -80: [03:04:13] Could not find RLabel mapping for atom: 0 in template: 1 -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. -80: [03:04:13] reactant 1 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] reactant 0 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] product 0 has no mapped atoms. +80: [12:10:19] Could not find RLabel mapping for atom: 0 in template: 1 +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. +80: [12:10:19] reactant 1 has no mapped atoms. 80: () 80: ******************************************** 80: $RXN @@ -21659,7 +21932,7 @@ 80: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 80: .. 80: ---------------------------------------------------------------------- -80: Ran 4 tests in 0.025s +80: Ran 4 tests in 0.050s 80: 80: OK 80: $RXN @@ -21706,410 +21979,192 @@ 80: M END 80: 80: $RXN Failed -78: ../build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:515: DeprecationWarning: Please use assertTrue instead. -78: self.failUnless(rxn) -78: [03:04:13] reactant 2 has no mapped atoms. -78: [03:04:13] reactant 2 has no mapped atoms. -78: [03:04:13] 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) -82: [03:04:13] Incomplete atom labelling, cannot make bond -82: [03:04:13] Incomplete atom labelling, cannot make bond -82: [03:04:13] Incomplete atom labelling, cannot make bond -82: [03:04:13] -82: -82: **** -82: Invariant Violation -82: molzip: bond info already exists for end atom with label:1 -82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: !bond.b -82: **** -82: -78: ......[03:04:13] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -78: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -78: [03:04:13] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -78: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -78: .[03:04:13] reactant atom-mapping number 1 found multiple times. -78: [03:04:13] product atom-mapping number 2 not found in reactants. -78: [03:04:13] mapped atoms in the reactants were not mapped in the products. -78: unmapped numbers are: 4 -78: [03:04:13] product atom-mapping number 5 not found in reactants. -82: [03:04:13] Incomplete atom labelling, cannot make bond -82: [03:04:13] -82: -82: **** -82: Invariant Violation -82: molzip: bond info already exists for end atom with label:1 -82: Violation occurred on line 982 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: !bond.b -82: **** -82: -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) -82: [03:04:13] -82: -82: **** -82: Invariant Violation -82: molzip: zipped Bond already exists, perhaps labels are duplicated -82: Violation occurred on line 738 in file ./Code/GraphMol/ChemTransforms/MolFragmenter.cpp -82: Failed Expression: params.label == MolzipLabel::FragmentOnBonds || !a->getOwningMol().getBondBetweenAtoms(a->getIdx(), b->getIdx()) -82: **** -82: -82: =============================================================================== -82: All tests passed (531 assertions in 4 test cases) -82: -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 - 70/208 Test #82: chemTransformsTestCatch ................ Passed 0.24 sec -test 85 - Start 85: testSubgraphs1 - -85: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -85: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -85: Test timeout computed to be: 1500 -85: ----------------------- -85: Subgraph retrieval -85: Finished -85: ----------------------- -85: testSubgraphs2a - 71/208 Test #80: pyChemReactionSanitize ................. Passed 0.50 sec -test 86 - Start 86: testSubgraphs2 - -86: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 -86: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Subgraphs -86: Test timeout computed to be: 1500 -78: ..[03:04:13] SMARTS Parse Error: syntax error while parsing: boromicacid -78: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -78: [03:04:13] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -78: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -78: [03:04:13] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -78: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -78: [03:04:13] reaction has no reactants -78: [03:04:13] reaction has no products -78: [03:04:13] initialization failed -85: Finished -85: ----------------------- -85: testSubgraphs2 -78: [03:04:13] reaction has no reactants -78: [03:04:13] reaction has no products -78: .[03:04:13] SMARTS Parse Error: syntax error while parsing: boromicacid -78: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -78: [03:04:13] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -78: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -78: [03:04:13] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -78: [03:04:13] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -78: [03:04:13] reaction has no reactants -78: [03:04:13] reaction has no products -78: [03:04:13] initialization failed -78: [03:04:13] reaction has no reactants -78: [03:04:13] reaction has no products -78: . -78: ---------------------------------------------------------------------- -78: Ran 45 tests in 0.176s -78: -78: OK -78: ******************************************** -78: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -78: -86: ----------------------- -86: Test1: pathToSubmol -86: Finished -86: ----------------------- -86: Test2: Atom Environments -86: Finished -86: ----------------------- -86: Test 3: Atom Environments (Extension) -86: Finished -86: ----------------------- -86: Testing github Issue103: stereochemistry and pathToSubmol -86: Finished -86: ----------------------- -86: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) -86: Finished - 72/208 Test #86: testSubgraphs2 ......................... Passed 0.07 sec -test 87 - Start 87: filterCatalogTest - -87: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -87: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog -87: Test timeout computed to be: 1500 -85: Finished -85: ----------------------- -85: Path retrieval -85: Finished -85: ----------------------- -85: Path retrieval2 -85: Finished -85: ----------------------- -85: Unique Subgraph retrieval -85: Finished -85: ----------------------- -85: testUniqueSubgraphs2 - 73/208 Test #78: pyChemReactions ........................ Passed 0.75 sec -test 88 - Start 88: pyFilterCatalog - -88: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -88: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -88: Test timeout computed to be: 1500 -79: [03:04:13] == 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) -87: Warning: molecule failed filter -87: Warning: molecule failed filter: reason hzone_phenol_A(479) -87: v = { -87: 0,23}, -87: 1,22}, -87: 2,20}, -87: 3,19}, -87: 4,25}, -87: 5,24}, -87: 6,18}, -87: 7,17}, -87: 8,16}, -87: 9,21}, -87: } -87: match = { -87: 0,23}, -87: 1,22}, -87: 2,20}, -87: 3,19}, -87: 4,25}, -87: 5,24}, -87: 6,18}, -87: 7,17}, -87: 8,16}, -87: 9,21}, -87: } -83: =============================================================================== -83: All tests passed (86 assertions in 12 test cases) -83: -87: Warning: molecule failed filter -87: Warning: molecule failed filter: reason cyano_imine_B(17) -87: v = { -87: 0,11}, -87: 1,12}, -87: 2,13}, -87: 3,14}, -87: 4,15}, -87: 5,10}, -87: 6,9}, -87: 7,8}, -87: 8,7}, -87: 9,6}, -87: 10,5}, -87: 11,17}, -87: 12,16}, -87: } -87: match = { -87: 0,11}, -87: 1,12}, -87: 2,13}, -87: 3,14}, -87: 4,15}, -87: 5,10}, -87: 6,9}, -87: 7,8}, -87: 8,7}, -87: 9,6}, -87: 10,5}, -87: 11,17}, -87: 12,16}, -87: } -87: Warning: molecule failed filter -79: .[03:04:13] == testEnumerateLibrary - 74/208 Test #83: tautomerQueryTestCatch ................. Passed 0.45 sec +79: .[12:10:19] == testRandomSampleAllBBs +87: O=C(Cn1cnc2c1c(=O)n(C)c(=O)n2C)N/N=C/c1c(O)ccc2c1cccc2 hzone_phenol_A(479) http://chemistrycompass.com/chemsearch/58909/ +87: FC(F)(F)Oc1ccc(NN=C(C#N)C#N)cc1 cyano_imine_B(17) CHEMBL457504 +87: O=C1C2OC2C(=O)c3cc4CCCCc4cc13 keto_keto_gamma(5) CHEMBL476649 +79: .[12:10:19] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +79: [12:10:19] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +79: .[12:10:19] == testRemoveBadMatches +79: .[12:10:19] == testTimings +87: 0 hzone_phenol_A(479) +87: 1 cyano_imine_B(17) +87: 2 keto_keto_gamma(5) +78: ..[12:10:20] SMARTS Parse Error: syntax error while parsing: boromicacid +78: [12:10:20] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' + 73/208 Test #87: filterCatalogTest ...................... Passed 0.40 sec test 89 Start 89: testFragCatalog 89: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 89: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog 89: Test timeout computed to be: 1500 -87: Warning: molecule failed filter: reason keto_keto_gamma(5) -87: v = { -87: 0,0}, -87: 1,1}, -87: 2,2}, -87: 3,4}, -87: 4,5}, -87: 5,6}, -87: 6,7}, -87: 7,8}, -87: 8,9}, -87: 9,14}, -87: 10,15}, -87: 11,16}, -87: } -87: match = { -87: 0,0}, -87: 1,1}, -87: 2,2}, -87: 3,4}, -87: 4,5}, -87: 5,6}, -87: 6,7}, -87: 7,8}, -87: 8,9}, -87: 9,14}, -87: 10,15}, -87: 11,16}, -87: } -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 -89: 21 -87: O=C(Cn1cnc2c1c(=O)n(C)c(=O)n2C)N/N=C/c1c(O)ccc2c1cccc2 hzone_phenol_A(479) http://chemistrycompass.com/chemsearch/58909/ -87: FC(F)(F)Oc1ccc(NN=C(C#N)C#N)cc1 cyano_imine_B(17) CHEMBL457504 -87: O=C1C2OC2C(=O)c3cc4CCCCc4cc13 keto_keto_gamma(5) CHEMBL476649 -79: ..[03:04:13] == testRGroupState -85: Finished -85: ----------------------- -85: testRootedSubgraphs -85: Finished -85: ----------------------- -85: testRootedPaths -85: Finished - 75/208 Test #85: testSubgraphs1 ......................... Passed 0.41 sec +78: [12:10:20] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +78: [12:10:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +78: [12:10:20] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +78: [12:10:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +78: [12:10:20] reaction has no reactants +78: [12:10:20] reaction has no products +78: [12:10:20] initialization failed +78: [12:10:20] reaction has no reactants +78: [12:10:20] reaction has no products +78: .[12:10:20] SMARTS Parse Error: syntax error while parsing: boromicacid +78: [12:10:20] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +78: [12:10:20] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +78: [12:10:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +78: [12:10:20] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +78: [12:10:20] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' + 74/208 Test #80: pyChemReactionSanitize ................. Passed 1.08 sec test 90 Start 90: pyFragCatalog 90: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 90: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 90: Test timeout computed to be: 1500 -79: .[03:04:13] == testRandomEnumerateAllBBsLibrary -87: 0 hzone_phenol_A(479) -87: 1 cyano_imine_B(17) -87: 2 keto_keto_gamma(5) -79: ** [1, 1] -79: ** [0, 2] -79: ** [1, 0] -79: .[03:04:13] == testRandomEnumerateLibrary - 76/208 Test #87: filterCatalogTest ...................... Passed 0.37 sec +78: [12:10:20] reaction has no reactants +78: [12:10:20] reaction has no products +78: [12:10:20] initialization failed +78: [12:10:20] reaction has no reactants +78: [12:10:20] reaction has no products +78: . +78: ---------------------------------------------------------------------- +78: Ran 45 tests in 0.469s +78: +78: OK +78: ******************************************** +78: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +78: +89: 21 + 75/208 Test #78: pyChemReactions ........................ Passed 1.66 sec test 91 Start 91: testDescriptors 91: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 91: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 91: Test timeout computed to be: 1500 -79: .[03:04:14] == testRandomSample -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test Crippen parameter acquisition. -79: .[03:04:14] == testRandomSampleAllBBs -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test Crippen calculation. -79: .[03:04:14] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -79: [03:04:14] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -79: .[03:04:14] == testRemoveBadMatches -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test Issue262: problems with Crippen calculation from pickles. -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test AMW calculation. -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test Exact MW calculation. -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test Labute ASA descriptors. -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test TPSA descriptors. +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test Crippen parameter acquisition. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test Crippen calculation. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test Issue262: problems with Crippen calculation from pickles. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test AMW calculation. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test Exact MW calculation. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test Labute ASA descriptors. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test TPSA descriptors. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test Lipinski parameters. +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") 84: ..... 84: ---------------------------------------------------------------------- -84: Ran 5 tests in 0.104s +84: Ran 5 tests in 0.212s 84: 84: OK -79: .[03:04:14] == testTimings -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test Lipinski parameters. - 77/208 Test #84: pyTautomerQuery ........................ Passed 0.82 sec +85: Finished +85: ----------------------- +85: testRootedSubgraphs +85: Finished +85: ----------------------- +85: testRootedPaths +85: Finished + 76/208 Test #85: testSubgraphs1 ......................... Passed 1.02 sec test 92 Start 92: testAUTOCORR2D 92: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 92: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 92: 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") -92: [03:04:14] ---------------------------- +92: [12:10:20] ---------------------------- 92: start test autocorr2D -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test VSA descriptors. -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test molecular formula calculation. -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test Issue 3415534. -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test Issue3433771: Bad definition for Crippen atom type O11. -91: [03:04:14] done -91: [03:04:14] ------------------------------------- -91: [03:04:14] Test multithreading +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test VSA descriptors. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test molecular formula calculation. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test Issue 3415534. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test Issue3433771: Bad definition for Crippen atom type O11. +91: [12:10:20] done +91: [12:10:20] ------------------------------------- +91: [12:10:20] Test multithreading 91: reading molecules +90: ......... +90: ---------------------------------------------------------------------- +90: Ran 9 tests in 0.152s +90: +90: OK 91: processing 91: launch :0 91: launch :1 91: launch :2 91: launch :3 -58: [03:04:14] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [03:04:14] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [03:04:14] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [03:04:14] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [03:04:14] 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: [03:04:14] -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: -90: ......... -90: ---------------------------------------------------------------------- -90: Ran 9 tests in 0.145s -90: -90: OK - 78/208 Test #90: pyFragCatalog .......................... Passed 0.87 sec + 77/208 Test #84: pyTautomerQuery ........................ Passed 1.35 sec test 93 Start 93: testATF 93: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testATF 93: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 93: Test timeout computed to be: 1500 - 79/208 Test #93: testATF ................................ Passed 0.07 sec + 78/208 Test #90: pyFragCatalog .......................... Passed 0.69 sec test 94 Start 94: testBCUT 94: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 94: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 94: Test timeout computed to be: 1500 -94: [03:04:14] ------------------------------------- -94: [03:04:14] Basic BCUT tests. -94: [03:04:14] done -94: [03:04:14] ------------------------------------- -94: [03:04:14] Larger BCUT tests. -92: [03:04:15] done -92: [03:04:15] ------------------------------------- -92: [03:04:15] Test Github #3806: NaNs from AUTOCORR2D descriptor -92: [03:04:15] done - 80/208 Test #92: testAUTOCORR2D ......................... Passed 0.82 sec +94: [12:10:20] ------------------------------------- +94: [12:10:20] Basic BCUT tests. + 79/208 Test #93: testATF ................................ Passed 0.13 sec test 95 Start 95: testEEM 95: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testEEM 95: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 95: Test timeout computed to be: 1500 -89: [03:04:15] +94: [12:10:20] done +94: [12:10:20] ------------------------------------- +94: [12:10:20] Larger BCUT tests. +92: [12:10:21] done +92: [12:10:21] ------------------------------------- +92: [12:10:21] Test Github #3806: NaNs from AUTOCORR2D descriptor +92: [12:10:21] done + 80/208 Test #92: testAUTOCORR2D ......................... Passed 1.09 sec +test 96 + Start 96: testPBF + +96: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF +96: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +96: Test timeout computed to be: 1500 +96: [12:10:21] ------------------------------------- +96: [12:10:21] Basic PBF tests. +96: [12:10:21] done +96: [12:10:21] ------------------------------------- +96: [12:10:21] PBF edge cases. +96: [12:10:21] done + 81/208 Test #96: testPBF ................................ Passed 0.31 sec +test 97 + Start 97: testRDFcustom + +97: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom +97: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +97: Test timeout computed to be: 1500 +89: [12:10:22] 89: 89: **** 89: Invariant Violation @@ -22118,7 +22173,7 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: -89: [03:04:15] +89: [12:10:22] 89: 89: **** 89: Invariant Violation @@ -22127,7 +22182,7 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: -89: [03:04:15] +89: [12:10:22] 89: 89: **** 89: Invariant Violation @@ -22136,117 +22191,128 @@ 89: Failed Expression: token != tokens.end() 89: **** 89: - 81/208 Test #89: testFragCatalog ........................ Passed 1.72 sec -test 96 - Start 96: testPBF - -96: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testPBF -96: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -96: Test timeout computed to be: 1500 -88: ...........[03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -88: [03:04:15] SMILES Parse Error: syntax error while parsing: --- -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [03:04:15] dasfsadf -96: [03:04:15] ------------------------------------- -96: [03:04:15] Basic PBF tests. -88: .[03:04:15] SMILES Parse Error: syntax error while parsing: mydoghasfleas -88: [03:04:15] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' - 82/208 Test #94: testBCUT ............................... Passed 0.89 sec -test 97 - Start 97: testRDFcustom + 82/208 Test #89: testFragCatalog ........................ Passed 2.09 sec +test 98 + Start 98: testRDF -97: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom -97: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -97: Test timeout computed to be: 1500 +98: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF +98: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors +98: Test timeout computed to be: 1500 +88: ...........[12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +88: [12:10:22] SMILES Parse Error: syntax error while parsing: --- +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [12:10:22] dasfsadf +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +79: . +79: ---------------------------------------------------------------------- +79: Ran 11 tests in 2.862s +79: +79: OK +79: True +79: == CartesianProductStrategy CartesianProductStrategy +79: 197 out of 300 +79: 0 6 out of 10 +79: 1 3 out of 5 +79: 2 4 out of 6 +79: 198 out of 300 +79: 0 10 out of 10 +79: 1 5 out of 5 +79: 2 6 out of 6 +79: Skipped 10000000 in 0.21077370643615723 seconds +79: Skipped 10000000 in 1.4429688453674316 seconds +79: Skipped 10000000 in 0.3959474563598633 seconds +88: .[12:10:22] SMILES Parse Error: syntax error while parsing: mydoghasfleas +88: [12:10:22] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +25: All 191 tests passed 88: ...... 88: ---------------------------------------------------------------------- -88: Ran 20 tests in 1.589s +88: Ran 20 tests in 2.159s 88: 88: OK 88: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -22268,110 +22334,79 @@ 88: 1 88: 2 88: running - 83/208 Test #88: pyFilterCatalog ........................ Passed 2.22 sec -test 98 - Start 98: testRDF - -98: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testRDF -98: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors -98: Test timeout computed to be: 1500 95: =>start test EEM 95: 0 95: 100 95: 200 95: 300 95: 400 -95: Elapsed time: 0.845344 s +95: Elapsed time: 1.5751 s 95: Errors:0 -95: [03:04:15] test on : 500 molecules done - 84/208 Test #95: testEEM ................................ Passed 0.90 sec +95: [12:10:22] test on : 500 molecules done + 83/208 Test #95: testEEM ................................ Passed 1.68 sec test 99 Start 99: testMORSE 99: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 99: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 99: Test timeout computed to be: 1500 -96: [03:04:16] done -96: [03:04:16] ------------------------------------- -96: [03:04:16] PBF edge cases. -96: [03:04:16] done - 85/208 Test #96: testPBF ................................ Passed 0.51 sec + 84/208 Test #94: testBCUT ............................... Passed 1.80 sec test 100 Start 100: test3D 100: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/test3D 100: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 100: Test timeout computed to be: 1500 -100: [03:04:16] ------------------------------------- -100: [03:04:16] Basic PMI tests. -79: . -79: ---------------------------------------------------------------------- -79: Ran 11 tests in 2.582s -79: -79: OK -79: True -79: == CartesianProductStrategy CartesianProductStrategy -79: 197 out of 300 -79: 0 6 out of 10 -79: 1 3 out of 5 -79: 2 4 out of 6 -79: 198 out of 300 -79: 0 10 out of 10 -79: 1 5 out of 5 -79: 2 6 out of 6 -79: Skipped 10000000 in 0.14886236190795898 seconds -79: Skipped 10000000 in 1.4796123504638672 seconds -79: Skipped 10000000 in 0.33240437507629395 seconds - 86/208 Test #79: pyChemReactionEnumerations ............. Passed 3.52 sec + 85/208 Test #79: pyChemReactionEnumerations ............. Passed 3.90 sec test 101 Start 101: testWHIM 101: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 101: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -100: [03:04:16] done -100: [03:04:16] ------------------------------------- -100: [03:04:16] More PMI/NPR tests. -100: [03:04:16] done -100: [03:04:16] ------------------------------------- -100: [03:04:16] Basic NPR tests. -100: [03:04:16] done -100: [03:04:16] ------------------------------------- -100: [03:04:16] PMI edge cases. -100: [03:04:16] done -100: [03:04:16] ------------------------------------- -100: [03:04:16] NPR edge cases. -100: [03:04:16] done -100: [03:04:16] ------------------------------------- -100: [03:04:16] 3D descriptors. -100: [03:04:16] done -100: [03:04:16] ------------------------------------- -100: [03:04:16] 3D descriptor edge cases. -100: [03:04:16] done -100: [03:04:16] ------------------------------------- -100: [03:04:16] Inertial shape factor. -100: [03:04:16] done - 87/208 Test #100: test3D ................................. Passed 0.87 sec +100: [12:10:22] ------------------------------------- +100: [12:10:22] Basic PMI tests. + 86/208 Test #88: pyFilterCatalog ........................ Passed 3.06 sec test 102 Start 102: testGETAWAY 102: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 102: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +100: [12:10:23] done +100: [12:10:23] ------------------------------------- +100: [12:10:23] More PMI/NPR tests. +100: [12:10:23] done +100: [12:10:23] ------------------------------------- +100: [12:10:23] Basic NPR tests. 101: =>start test WHIM -101: [03:04:17] test on : 365 molecules done - 88/208 Test #101: testWHIM ............................... Passed 0.89 sec +101: [12:10:23] test on : 365 molecules done + 87/208 Test #101: testWHIM ............................... Passed 0.96 sec test 103 Start 103: testAUTOCORR3D 103: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 103: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 -99: =>start test MORSE -99: =>read file -99: [03:04:17] test on : 365 molecules done - 89/208 Test #99: testMORSE .............................. Passed 1.56 sec +100: [12:10:23] done +100: [12:10:23] ------------------------------------- +100: [12:10:23] PMI edge cases. +100: [12:10:23] done +100: [12:10:23] ------------------------------------- +100: [12:10:23] NPR edge cases. +100: [12:10:23] done +100: [12:10:23] ------------------------------------- +100: [12:10:23] 3D descriptors. +100: [12:10:23] done +100: [12:10:23] ------------------------------------- +100: [12:10:23] 3D descriptor edge cases. +100: [12:10:23] done +100: [12:10:23] ------------------------------------- +100: [12:10:23] Inertial shape factor. +100: [12:10:23] done + 88/208 Test #100: test3D ................................. Passed 1.26 sec test 104 Start 104: testCoulombMat @@ -22379,10 +22414,8 @@ 104: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Descriptors 104: Test timeout computed to be: 1500 104: ===================== Testing CoulombMat ======================= -97: =>start test rdf custom -97: [03:04:17] test on : 365 molecules done 104: CM test 1 mat Done - 90/208 Test #104: testCoulombMat ......................... Passed 0.10 sec + 89/208 Test #104: testCoulombMat ......................... Passed 0.09 sec test 105 Start 105: descriptorsTestCatch @@ -22392,21 +22425,27 @@ 105: =============================================================================== 105: All tests passed (130 assertions in 5 test cases) 105: - 91/208 Test #105: descriptorsTestCatch ................... Passed 0.09 sec + 90/208 Test #105: descriptorsTestCatch ................... Passed 0.10 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-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap 106: Test timeout computed to be: 1500 - 92/208 Test #39: resMolSupplierTest ..................... Passed 6.25 sec +97: =>start test rdf custom +97: [12:10:24] test on : 365 molecules done +103: =>start test autocorr3D +103: [12:10:24] test on : 365 molecules done + 91/208 Test #103: testAUTOCORR3D ......................... Passed 1.07 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-x86_64-linux-gnu/Code/GraphMol/Descriptors/Wrap 107: Test timeout computed to be: 1500 - 93/208 Test #37: hanoiTest .............................. Passed 6.49 sec +98: =>start test rdf +98: [12:10:24] test on : 365 molecules done + 92/208 Test #98: testRDF ................................ Passed 2.60 sec test 108 Start 108: testFingerprints @@ -22693,6 +22732,15 @@ 108: SMI: n1c[nH]c2cc(O)nc(O)c21 108: Atoms: 108: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 +106: .....[12:10:24] +106: +106: **** +106: Pre-condition Violation +106: Number of atom props not equal to number of atoms +106: Violation occurred on line 83 in file ./Code/GraphMol/Descriptors/BCUT.cpp +106: Failed Expression: atom_props.size() == num_atoms +106: **** +106: 108: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 108: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 108: 3 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 @@ -22896,244 +22944,38 @@ 108: 108: ------------------- 108: -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Morgan Fingerprints. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Morgan Fingerprints using fromAtoms argument. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Morgan Fingerprints as bit vects. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Morgan Fingerprints with feature invariants. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test additional Morgan fingerprints options. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Atom Codes. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Atom Pairs. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Atom Pairs part 2. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Topological Torsions. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Bulk Topological Torsions. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Hashed Atom Pairs. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Hashed torsions. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Rooted Atom Pairs. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test ignoring atoms in Atom Pairs. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Rooted Topological Torsions. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test ignoring atoms in Topological Torsions. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test atom info from morgan fingerprints. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test atom info from morgan fingerprints including Info Redundant Environments. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] ------------------------------------- -108: [03:04:18] ------------------------------------- -108: [03:04:18] ------------------------------------- -108: [03:04:18] ------------------------------------- -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Atom Pairs including info about chirality. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test Topological Torsions including info about chirality. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test GitHub Issue 25: fingerprint backwards compatibility. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test GitHub Issue 151: PatternFingerprint problems -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test 3D atom pairs. -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -108: [03:04:18] done -108: [03:04:18] ------------------------------------- -108: [03:04:18] Test multithreading with the pattern FP -108: reading molecules -103: =>start test autocorr3D -103: [03:04:18] test on : 365 molecules done - 94/208 Test #103: testAUTOCORR3D ......................... Passed 0.95 sec -test 109 - Start 109: testMHFPFingerprint - -109: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -109: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -109: Test timeout computed to be: 1500 -108: pass 1 -108: launch :0 -108: launch :1 -108: launch :2 -108: launch :3 -109: [03:04:18] ------------------------------------- -109: [03:04:18] Test MHFP fingerprint encoder initialization -109: [03:04:18] done -109: [03:04:18] ------------------------------------- -109: [03:04:18] Test MHFP shingling creation -109: [03:04:18] done -109: [03:04:18] ------------------------------------- -109: [03:04:18] Test MHFP hashing of string and uint arrays -109: [03:04:18] done -109: [03:04:18] ------------------------------------- -109: [03:04:18] Test SECFP fingerprint functionality -109: [03:04:18] done - 95/208 Test #109: testMHFPFingerprint .................... Passed 0.17 sec -test 110 - Start 110: testFingerprintGenerators - -110: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -110: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -110: Test timeout computed to be: 1500 -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test atom-pair fp generator -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test atom-pair fp generator with different arguments -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -11: .................. -11: ---------------------------------------------------------------------- -11: Ran 18 tests in 7.359s -11: -11: OK -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test atom-pair additional output -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test Folded Atom Pairs. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test Rooted Atom Pairs. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test ignoring atoms in Atom Pairs. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test Atom Pairs including info about chirality. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test Morgan Fingerprints. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test morgan fp generator -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test Morgan Fingerprints using fromAtoms argument. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test Morgan Fingerprints as bit vects. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test Morgan Fingerprints with feature invariants. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test additional Morgan fingerprints options. -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Single atoms setting radius 1 bits in Morgan fingerprints -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test different invariant generator combinations -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test invariant overriding -110: [03:04:18] done -110: [03:04:18] ------------------------------------- -110: [03:04:18] Test RDKit fp generator - 96/208 Test #11: pyBV ................................... Passed 8.05 sec -test 111 - Start 111: fpTestCatch - -111: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch -111: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints -111: Test timeout computed to be: 1500 -107: ........ -107: ---------------------------------------------------------------------- -107: Ran 8 tests in 0.402s -107: -107: OK -98: =>start test rdf -98: [03:04:18] test on : 365 molecules done - 97/208 Test #98: testRDF ................................ Passed 2.83 sec -test 112 - Start 112: pyTestGenerator - -112: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" -112: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap -112: Test timeout computed to be: 1500 -111: =============================================================================== -111: All tests passed (163 assertions in 13 test cases) -111: -97: =>start test morse custom -97: [03:04:18] test on : 365 molecules done - 98/208 Test #111: fpTestCatch ............................ Passed 0.09 sec -test 113 - Start 113: pyTestMHFP - -113: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" -113: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap -113: Test timeout computed to be: 1500 -108: pass 2 -108: launch :0 -108: launch :1 -108: launch :2 -108: launch :3 - 99/208 Test #107: pyMolDescriptors3D ..................... Passed 1.07 sec -test 114 - Start 114: testPartialCharges - -114: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges -114: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges -114: Test timeout computed to be: 1500 -100/208 Test #114: testPartialCharges ..................... Passed 0.04 sec -test 115 - Start 115: pyPartialCharges - -115: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" -115: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap -115: Test timeout computed to be: 1500 -106: .....[03:04:18] -106: -106: **** -106: Pre-condition Violation -106: Number of atom props not equal to number of atoms -106: Violation occurred on line 83 in file ./Code/GraphMol/Descriptors/BCUT.cpp -106: Failed Expression: atom_props.size() == num_atoms -106: **** -106: +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Morgan Fingerprints. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Morgan Fingerprints using fromAtoms argument. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Morgan Fingerprints as bit vects. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Morgan Fingerprints with feature invariants. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test additional Morgan fingerprints options. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Atom Codes. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Atom Pairs. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Atom Pairs part 2. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Topological Torsions. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Bulk Topological Torsions. 106: ........................ 106: ---------------------------------------------------------------------- -106: Ran 29 tests in 0.051s +106: Ran 29 tests in 0.069s 106: 106: OK 106: exactmw 78.046950192 @@ -23181,13 +23023,249 @@ 106: Phi 0.9130327103921437 106: exactmw 78.046950192 106: lipinskiHBA 0.0 -101/208 Test #106: pyMolDescriptors ....................... Passed 1.26 sec +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Hashed Atom Pairs. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Hashed torsions. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Rooted Atom Pairs. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test ignoring atoms in Atom Pairs. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Rooted Topological Torsions. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test ignoring atoms in Topological Torsions. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test atom info from morgan fingerprints. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test atom info from morgan fingerprints including Info Redundant Environments. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] ------------------------------------- +108: [12:10:24] ------------------------------------- +108: [12:10:24] ------------------------------------- +108: [12:10:24] ------------------------------------- +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Atom Pairs including info about chirality. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test Topological Torsions including info about chirality. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test GitHub Issue 25: fingerprint backwards compatibility. +108: [12:10:24] done +108: [12:10:24] ------------------------------------- +108: [12:10:24] Test GitHub Issue 151: PatternFingerprint problems + 93/208 Test #106: pyMolDescriptors ....................... Passed 0.98 sec +test 109 + Start 109: testMHFPFingerprint + +109: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +109: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +109: Test timeout computed to be: 1500 +108: [12:10:25] done +108: [12:10:25] ------------------------------------- +108: [12:10:25] Test 3D atom pairs. +108: [12:10:25] done +108: [12:10:25] ------------------------------------- +108: [12:10:25] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +108: [12:10:25] done +108: [12:10:25] ------------------------------------- +108: [12:10:25] Test multithreading with the pattern FP +108: reading molecules + 94/208 Test #37: hanoiTest .............................. Passed 8.07 sec +test 110 + Start 110: testFingerprintGenerators + +110: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +110: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +110: Test timeout computed to be: 1500 +109: [12:10:25] ------------------------------------- +109: [12:10:25] Test MHFP fingerprint encoder initialization +108: pass 1 +108: launch :0 +108: launch :1 +108: launch :2 +108: launch :3 +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test atom-pair fp generator +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test atom-pair fp generator with different arguments +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +109: [12:10:25] done +109: [12:10:25] ------------------------------------- +109: [12:10:25] Test MHFP shingling creation +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test atom-pair additional output +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Folded Atom Pairs. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Rooted Atom Pairs. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test ignoring atoms in Atom Pairs. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Atom Pairs including info about chirality. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Morgan Fingerprints. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test morgan fp generator +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Morgan Fingerprints using fromAtoms argument. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Morgan Fingerprints as bit vects. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Morgan Fingerprints with feature invariants. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test additional Morgan fingerprints options. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Single atoms setting radius 1 bits in Morgan fingerprints +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test different invariant generator combinations +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test invariant overriding +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test RDKit fp generator +109: [12:10:25] done +109: [12:10:25] ------------------------------------- +109: [12:10:25] Test MHFP hashing of string and uint arrays +109: [12:10:25] done +109: [12:10:25] ------------------------------------- +109: [12:10:25] Test SECFP fingerprint functionality +109: [12:10:25] done + 95/208 Test #109: testMHFPFingerprint .................... Passed 0.14 sec +test 111 + Start 111: fpTestCatch + +111: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch +111: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints +111: Test timeout computed to be: 1500 +111: =============================================================================== +111: All tests passed (163 assertions in 13 test cases) +111: + 96/208 Test #111: fpTestCatch ............................ Passed 0.09 sec +test 112 + Start 112: pyTestGenerator + +112: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" +112: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap +112: Test timeout computed to be: 1500 +99: =>start test MORSE +99: =>read file +99: [12:10:25] test on : 365 molecules done + 97/208 Test #99: testMORSE .............................. Passed 2.82 sec +test 113 + Start 113: pyTestMHFP + +113: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" +113: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Fingerprints/Wrap +113: Test timeout computed to be: 1500 +108: pass 2 +108: launch :0 +108: launch :1 +108: launch :2 +108: launch :3 +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test unfolded version of RDKFP +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test topological torsion fp generator +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Topological Torsions. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Folded torsions. +110: [12:10:25] done +110: [12:10:25] ------------------------------------- +110: [12:10:25] Test Bulk Topological Torsions. +107: ........ +107: ---------------------------------------------------------------------- +107: Ran 8 tests in 0.564s +107: +107: OK +110: [12:10:26] done +110: [12:10:26] ------------------------------------- +110: [12:10:26] Test Rooted Topological Torsions. +110: [12:10:26] done +110: [12:10:26] ------------------------------------- +110: [12:10:26] Test ignoring atoms in Topological Torsions. +110: [12:10:26] done +110: [12:10:26] ------------------------------------- +110: [12:10:26] ------------------------------------- +110: [12:10:26] Test Topological Torsions including info about chirality. +110: [12:10:26] done +110: [12:10:26] ------------------------------------- +110: [12:10:26] Test GitHub Issue 25: fingerprint backwards compatibility. +110: [12:10:26] done +110: [12:10:26] ------------------------------------- +110: [12:10:26] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +110: [12:10:26] done +110: [12:10:26] ------------------------------------- +110: [12:10:26] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +110: [12:10:26] Warning: molecule is tagged as 3D, but all Z coords are zero +110: [12:10:26] done +110: [12:10:26] ------------------------------------- +110: [12:10:26] Test convenience and bulk fp calculation functions +112: ......... +112: ---------------------------------------------------------------------- +112: Ran 9 tests in 0.129s +112: +112: OK + 98/208 Test #107: pyMolDescriptors3D ..................... Passed 1.59 sec +test 114 + Start 114: testPartialCharges + +114: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges +114: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges +114: Test timeout computed to be: 1500 + 99/208 Test #112: pyTestGenerator ........................ Passed 1.00 sec +test 115 + Start 115: pyPartialCharges + +115: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" +115: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/PartialCharges/Wrap +115: Test timeout computed to be: 1500 +100/208 Test #114: testPartialCharges ..................... Passed 0.07 sec test 116 Start 116: testMolTransforms 116: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 116: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms 116: Test timeout computed to be: 1500 +113: . +113: ---------------------------------------------------------------------- +113: Ran 1 test in 0.105s +113: +113: OK 116: *********************************************************** 116: Testing MolTransforms 116: --------------------------------- @@ -23218,167 +23296,66 @@ 116: testWeightedCentroid 116: 116: *********************************************************** -102/208 Test #116: testMolTransforms ...................... Passed 0.12 sec +101/208 Test #116: testMolTransforms ...................... Passed 0.12 sec test 117 Start 117: pyMolTransforms 117: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 117: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 117: Test timeout computed to be: 1500 -97: =>start test AUTOCORR3D custom -97: [03:04:19] test on : 365 molecules done -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test unfolded version of RDKFP -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test topological torsion fp generator -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test Topological Torsions. -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test Folded torsions. -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test Bulk Topological Torsions. -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test Rooted Topological Torsions. -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test ignoring atoms in Topological Torsions. -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test Topological Torsions including info about chirality. -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test GitHub Issue 25: fingerprint backwards compatibility. -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -110: [03:04:19] Warning: molecule is tagged as 3D, but all Z coords are zero -110: [03:04:19] done -110: [03:04:19] ------------------------------------- -110: [03:04:19] Test convenience and bulk fp calculation functions -112: ......... -112: ---------------------------------------------------------------------- -112: Ran 9 tests in 0.122s -112: -112: OK -97: =>start test 2 WHIM custom -97: [03:04:19] test on : 365 molecules done -58: [03:04:19] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:19] Warning: molecule is tagged as 3D, but all Z coords are zero -103/208 Test #112: pyTestGenerator ........................ Passed 0.87 sec +102/208 Test #113: pyTestMHFP ............................. Passed 1.09 sec test 118 Start 118: testMMFFForceFieldHelpers 118: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 118: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 118: Test timeout computed to be: 1500 -118: [03:04:19] ------------------------------------- -118: [03:04:19] Test MMFF atom types. -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing MMFF builder tools. -115: ....... -115: ---------------------------------------------------------------------- -115: Ran 7 tests in 0.231s -115: -115: OK -113: . -113: ---------------------------------------------------------------------- -113: Ran 1 test in 0.076s -113: -113: OK -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing MMFF builder+minimization. -58: ---------------------------------- -58: ---------------------------------- -58: [03:04:19] -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: [03:04:19] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing Issue239. -104/208 Test #115: pyPartialCharges ....................... Passed 0.95 sec +118: [12:10:26] ------------------------------------- +118: [12:10:26] Test MMFF atom types. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing MMFF builder tools. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing MMFF builder+minimization. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing Issue239. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing calcEnergy with passed coords. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing calcGrad. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing Issue242. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing github 308: crash during MMFF parameterization . +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing SFIssue1653802. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Testing SFIssue2378119. +118: [12:10:26] done +118: [12:10:26] ------------------------------------- +118: [12:10:26] Test MMFF force-field parameter getters. +118: [12:10:26] ------------------------------------- +118: [12:10:26] Test MMFF multithreading +118: generating reference data +110: [12:10:27] done +103/208 Test #110: testFingerprintGenerators .............. Passed 2.06 sec test 119 Start 119: testMMFFForceFieldHelpersMultiThread 119: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 119: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 119: Test timeout computed to be: 1500 -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing calcEnergy with passed coords. -105/208 Test #113: pyTestMHFP ............................. Passed 1.05 sec -test 120 - Start 120: testUFFForceFieldHelpers - -120: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -120: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -120: Test timeout computed to be: 1500 -25: All 191 tests passed -119: [03:04:19] ------------------------------------- -119: [03:04:19] Test MMFF multithreading -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing calcGrad. -120: [03:04:19] ------------------------------------- -120: [03:04:19] Test UFF atom labels. -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing Issue242. -120: [03:04:19] done -120: [03:04:19] ------------------------------------- -120: [03:04:19] Test UFF atom typer. -120: [03:04:19] done -120: [03:04:19] ------------------------------------- -120: [03:04:19] Testing UFF builder tools. -120: [03:04:19] done -120: [03:04:19] ------------------------------------- -120: [03:04:19] Testing UFF builder+minimization. -110: [03:04:19] done -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing github 308: crash during MMFF parameterization . -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing SFIssue1653802. -106/208 Test #110: testFingerprintGenerators .............. Passed 1.39 sec -test 121 - Start 121: testCrystalForceField - -121: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -121: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -121: Test timeout computed to be: 1500 -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Testing SFIssue2378119. -118: [03:04:19] done -118: [03:04:19] ------------------------------------- -118: [03:04:19] Test MMFF force-field parameter getters. -118: [03:04:19] ------------------------------------- -118: [03:04:19] Test MMFF multithreading -121: ------------------------------------- -121: Test CrystalFF torsional term. -117: ........ -117: ---------------------------------------------------------------------- -117: Ran 8 tests in 0.215s -117: -117: OK -118: generating reference data +119: [12:10:27] ------------------------------------- +119: [12:10:27] Test MMFF multithreading +97: =>start test morse custom +97: [12:10:27] test on : 365 molecules done 119: processing 119: launch :0 119: launch :1 @@ -23404,464 +23381,595 @@ 119: launch :21 119: launch :22 119: launch :23 -107/208 Test #117: pyMolTransforms ........................ Passed 0.99 sec +115: ....... +115: ---------------------------------------------------------------------- +115: Ran 7 tests in 0.265s +115: +115: OK +102: =>start test GETAWAY +102: [12:10:27] test on : 365 molecules done +104/208 Test #102: testGETAWAY ............................ Passed 4.62 sec +test 120 + Start 120: testUFFForceFieldHelpers + +120: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +120: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +120: Test timeout computed to be: 1500 +120: [12:10:27] ------------------------------------- +120: [12:10:27] Test UFF atom labels. +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Test UFF atom typer. +105/208 Test #115: pyPartialCharges ....................... Passed 1.18 sec +test 121 + Start 121: testCrystalForceField + +121: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +121: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +121: Test timeout computed to be: 1500 +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing UFF builder tools. +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing UFF builder+minimization. +121: ------------------------------------- +121: Test CrystalFF torsional term. +117: ........ +117: ---------------------------------------------------------------------- +117: Ran 8 tests in 0.423s +117: +117: OK +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test Issue252: Bad definitions for Crippen atom types. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test calculation of ChiVs. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test calculation of ChiNs. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test calculation of HallKierAlpha. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test calculation of Kappa1. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test calculation of Kappa2. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test calculation of Kappa3. +58: [12:10:27] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:27] Warning: molecule is tagged as 3D, but all Z coords are zero +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test Crippen atom type calculations. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test ring descriptors +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test other count descriptors. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test MQN +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test GitHub Issue 56. +91: [12:10:27] WARNING: not removing hydrogen atom without neighbors +91: [12:10:27] WARNING: not removing hydrogen atom without neighbors +91: [12:10:27] WARNING: not removing hydrogen atom without neighbors +91: [12:10:27] WARNING: not removing hydrogen atom without neighbors +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test Github92: Bad Crippen atom type for pyrrole H. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test Github362: order dependence in Kier-Hall descriptors. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test calculation of spiro and bridgehead counts. +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test Github694: ExactMolWt ignoring the mass of the electron +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Testing Properties and KitchenSink +91: [12:10:27] ---Caught keyerror (bad property name)--- +91: [12:10:27] ---Caught stereo value error--- +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test USR Descriptor +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test Github #1973: support P and S terms for TPSA calculation +91: [12:10:27] done +91: [12:10:27] ------------------------------------- +91: [12:10:27] Test Github #2948: Empty molecule has non-zero LabuteASA +91: [12:10:27] done +106/208 Test #91: testDescriptors ........................ Passed 7.40 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-x86_64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 122: Test timeout computed to be: 1500 -97: =>start test 1 WHIM custom -97: [03:04:20] test on : 365 molecules done -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Testing UFF special cases. -120: [03:04:20] UFFTYPER: Unrecognized charge state for atom: 0 -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Testing Issue239. -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -108/208 Test #121: testCrystalForceField .................. Passed 0.30 sec +107/208 Test #117: pyMolTransforms ........................ Passed 1.34 sec test 123 Start 123: testDistGeomHelpers 123: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 123: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 123: Test timeout computed to be: 1500 -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Testing calcEnergy with passed coords. -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Testing calcGrad. +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing UFF special cases. +120: [12:10:27] UFFTYPER: Unrecognized charge state for atom: 0 +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing Issue239. +58: ---------------------------------- +58: ---------------------------------- +58: [12:10:27] +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: [12:10:27] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing calcEnergy with passed coords. 123: go 123: ------------------------------------- 123: -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Testing SFIssue1653802. -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Testing SFIssue2378119. -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Test UFF force-field parameter getters. -120: [03:04:20] ------------------------------------- -120: [03:04:20] Testing handling missing parameters. -120: [03:04:20] UFFTYPER: Unrecognized hybridization for atom: 0 -120: [03:04:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) -120: [03:04:20] UFFTYPER: Unrecognized hybridization for atom: 0 -120: [03:04:20] UFFTYPER: Unrecognized atom type: Cu+1 (0) -58: [03:04:20] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -58: [03:04:20] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Testing SFIssue3009337. -120: [03:04:20] done -120: [03:04:20] ------------------------------------- -120: [03:04:20] Test UFF multithreading -120: generating reference data -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test Issue252: Bad definitions for Crippen atom types. -58: [03:04:20] Empty atom list: 'M ALS 1 0 F' on line 8. -58: de_DE.UTF-8 -58: [03:04:20] ------------------------------------- -58: [03:04:20] Test multithreading Locale Switching -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test calculation of ChiVs. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test calculation of ChiNs. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test calculation of HallKierAlpha. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test calculation of Kappa1. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test calculation of Kappa2. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test calculation of Kappa3. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test Crippen atom type calculations. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test ring descriptors -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test other count descriptors. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test MQN -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test GitHub Issue 56. -91: [03:04:20] WARNING: not removing hydrogen atom without neighbors -91: [03:04:20] WARNING: not removing hydrogen atom without neighbors -91: [03:04:20] WARNING: not removing hydrogen atom without neighbors -91: [03:04:20] WARNING: not removing hydrogen atom without neighbors -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test Github92: Bad Crippen atom type for pyrrole H. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test Github362: order dependence in Kier-Hall descriptors. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test calculation of spiro and bridgehead counts. -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test Github694: ExactMolWt ignoring the mass of the electron -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Testing Properties and KitchenSink -91: [03:04:20] ---Caught keyerror (bad property name)--- -91: [03:04:20] ---Caught stereo value error--- -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test USR Descriptor -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test Github #1973: support P and S terms for TPSA calculation -91: [03:04:20] done -91: [03:04:20] ------------------------------------- -91: [03:04:20] Test Github #2948: Empty molecule has non-zero LabuteASA -91: [03:04:20] done -109/208 Test #91: testDescriptors ........................ Passed 6.57 sec +119: done +97: =>start test AUTOCORR3D custom +97: [12:10:27] test on : 365 molecules done +108/208 Test #121: testCrystalForceField .................. Passed 0.44 sec test 124 Start 124: distGeomHelpersCatch 124: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 124: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers 124: Test timeout computed to be: 1500 -58: [03:04:20] Test multithreading (Done) -58: [03:04:20] ------------------------------------- -119: done -58: *************************************** -58: *************************************** -119: [03:04:20] done -58: [03:04:20] bond with order 0 found on line 7. This is not part of the MDL specification. -58: [03:04:20] unrecognized query bond type, 9, found on line 7. Using an "any" query. -110/208 Test #119: testMMFFForceFieldHelpersMultiThread ... Passed 0.91 sec +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing calcGrad. +119: [12:10:27] done +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing SFIssue1653802. +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing SFIssue2378119. +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Test UFF force-field parameter getters. +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing handling missing parameters. +120: [12:10:27] UFFTYPER: Unrecognized hybridization for atom: 0 +120: [12:10:27] UFFTYPER: Unrecognized atom type: Cu+1 (0) +120: [12:10:27] UFFTYPER: Unrecognized hybridization for atom: 0 +120: [12:10:27] UFFTYPER: Unrecognized atom type: Cu+1 (0) +109/208 Test #119: testMMFFForceFieldHelpersMultiThread ... Passed 0.88 sec test 125 Start 125: pyDistGeomHelpers 125: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 125: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 125: Test timeout computed to be: 1500 -58: [03:04:20] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -58: [03:04:20] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -58: [03:04:20] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:20] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:20] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:20] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:20] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:20] Warning: molecule is tagged as 3D, but all Z coords are zero -124: [03:04:20] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, (0, 100, 0, 0, 0, 0) -124: [03:04:20] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, (0, 0, 2.5, 0, 0, 0) -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 -124: [03:04:20] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, (0, 0, 7, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, (0, 0, 7, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, (0, 0, 7, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, (0, 0, 7, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, (0, 0, 7, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, (0, 0, 7, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, (0, 0, 7, 0, 0, 0) -124: [03:04:20] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, (0, 0, 7, 0, 0, 0) -124: [03:04:20] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, (-1, -0.5, -0.2, -0.3, 0, -0.3) -122: [03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -122: ..[03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -124: [03:04:20] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, (0, 3.6, 0, 0, 0, 0) -124: [03:04:20] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, (0, 100, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, (5, 0, 0, 0, 0, 0) -122: [03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -58: check isomorphism -124: [03:04:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, (100, 0, 0, 0, 0, 0) -124: [03:04:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, (0, 0, 1, 0, 0, 0) -124: [03:04:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, (0, 0, 1, 0, 0, 0) -124: [03:04:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, (0, 0, 1, 0, 0, 0) -124: [03:04:20] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, (0, 0, 1, 0, 0, 0) -124: [03:04:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, (0, 10, 0, 0, 0, 0) -124: [03:04:20] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [!#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: [03:04:20] [!#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: [03:04:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, (0, 3, 0, 0, 0, 0) -124: [03:04:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, (0, 3, 0, 0, 0, 0) -124: [03:04:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, (0, 3, 0, 0, 0, 0) -124: [03:04:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, (0, 3, 0, 0, 0, 0) -124: [03:04:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, (0, 3, 0, 0, 0, 0) -124: [03:04:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, (0, 3, 0, 0, 0, 0) -124: [03:04:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, (0, 3, 0, 0, 0, 0) -124: [03:04:20] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, (0, 3, 0, 0, 0, 0) +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Testing SFIssue3009337. +120: [12:10:27] done +120: [12:10:27] ------------------------------------- +120: [12:10:27] Test UFF multithreading +120: generating reference data +124: [12:10:28] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, (0, 100, 0, 0, 0, 0) +124: [12:10:28] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, (0, 0, 2.5, 0, 0, 0) +124: [12:10:28] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, (0, 0, 7, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, (0, 0, 7, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, (0, 0, 7, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, (0, 0, 7, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, (0, 0, 7, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, (0, 0, 7, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, (0, 0, 7, 0, 0, 0) +124: [12:10:28] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, (0, 0, 7, 0, 0, 0) +124: [12:10:28] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, (-1, -0.5, -0.2, -0.3, 0, -0.3) +124: [12:10:28] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, (0, 3.6, 0, 0, 0, 0) +124: [12:10:28] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, (0, 100, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, (100, 0, 0, 0, 0, 0) +124: [12:10:28] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, (0, 0, 1, 0, 0, 0) +124: [12:10:28] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, (0, 0, 1, 0, 0, 0) +124: [12:10:28] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, (0, 0, 1, 0, 0, 0) +124: [12:10:28] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, (0, 0, 1, 0, 0, 0) +124: [12:10:28] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, (0, 10, 0, 0, 0, 0) +124: [12:10:28] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [!#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: [12:10:28] [!#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: [12:10:28] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, (0, 3, 0, 0, 0, 0) +124: [12:10:28] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, (0, 3, 0, 0, 0, 0) +124: [12:10:28] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, (0, 3, 0, 0, 0, 0) +124: [12:10:28] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, (0, 3, 0, 0, 0, 0) +124: [12:10:28] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, (0, 3, 0, 0, 0, 0) +124: [12:10:28] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, (0, 3, 0, 0, 0, 0) +124: [12:10:28] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, (0, 3, 0, 0, 0, 0) +124: [12:10:28] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, (0, 3, 0, 0, 0, 0) 124: ----------- -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, (100, 0, 0, 0, 0, 0) -124: [03:04:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, (100, 0, 0, 0, 0, 0) -122: .[03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -124: [03:04:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, (0, 10, 0, 0, 0, 0) -124: [03:04:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, (0, 10, 0, 0, 0, 0) -124: [03:04:20] [!#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: [03:04:20] [!#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: [03:04:20] [!#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: [03:04:20] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, (0, 0, 1, 0, 0, 0) -124: [03:04:20] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, (0, 0, 1, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, (100, 0, 0, 0, 0, 0) +124: [12:10:28] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, (100, 0, 0, 0, 0, 0) +124: [12:10:28] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, (0, 10, 0, 0, 0, 0) +124: [12:10:28] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, (0, 10, 0, 0, 0, 0) +124: [12:10:28] [!#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: [12:10:28] [!#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: [12:10:28] [!#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: [12:10:28] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, (0, 0, 1, 0, 0, 0) +124: [12:10:28] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, (0, 0, 1, 0, 0, 0) 124: ----------- -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, (0, 0, 4, 0, 0, 0) -124: [03:04:20] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, (100, 0, 0, 0, 0, 0) -124: [03:04:20] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, (0, 10, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, (0, 0, 4, 0, 0, 0) +124: [12:10:28] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, (100, 0, 0, 0, 0, 0) +124: [12:10:28] 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: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, (0, 8, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, (5, 0, 0, 0, 0, 0) -124: [03:04:20] [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: [03:04:20] [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: [03:04:20] [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: [03:04:20] [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: [03:04:20] [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: [03:04:20] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, (0, 0, 2, 0, 0, 0) -122: .[03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[03:04:20] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[03:04:21] UFFTYPER: Unrecognized hybridization for atom: 0 -122: [03:04:21] UFFTYPER: Unrecognized atom type: Cu+1 (0) -122: .[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: ..[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -122: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, (0, 8, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, (5, 0, 0, 0, 0, 0) +124: [12:10:28] [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: [12:10:28] [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: [12:10:28] [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: [12:10:28] [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: [12:10:28] [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: [12:10:28] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, (0, 0, 2, 0, 0, 0) 118: processing 118: launch :0 118: launch :1 118: launch :2 118: launch :3 -124: [03:04:21] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -124: [03:04:21] UFFTYPER: Unrecognized atom type: N_5 (2) -124: [03:04:21] UFFTYPER: Unrecognized atom type: N_5 (3) -118: [03:04:21] Rep: 0 Mol:0 +118: [12:10:28] Rep: 0 Mol:0 +118: [12:10:28] Rep: 0 Mol:1 +118: [12:10:28] Rep: 0 Mol:2 +118: [12:10:28] Rep: 0 Mol:3 +118: [12:10:28] Rep: 0 Mol:5 +118: [12:10:28] Rep: 0 Mol:9 +118: [12:10:28] Rep: 0 Mol:4 +118: [12:10:28] Rep: 0 Mol:13 +118: [12:10:28] Rep: 0 Mol:17 +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: ..[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:28] Rep: 0 Mol:6 +118: [12:10:28] Rep: 0 Mol:8 +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:28] Rep: 0 Mol:10 +118: [12:10:28] Rep: 0 Mol:12 +118: [12:10:28] Rep: 0 Mol:16 +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:28] Rep: 0 Mol:7 +118: [12:10:28] Rep: 0 Mol:11 +118: [12:10:28] Rep: 0 Mol:15 +118: [12:10:28] Rep: 0 Mol:19 +118: [12:10:28] Rep: 0 Mol:20 +118: [12:10:28] Rep: 0 Mol:21 +118: [12:10:28] Rep: 0 Mol:23 +118: [12:10:28] Rep: 0 Mol:27 +118: [12:10:28] Rep: 0 Mol:24 +118: [12:10:28] Rep: 0 Mol:25 +118: [12:10:28] Rep: 0 Mol:31 +118: [12:10:28] Rep: 0 Mol:28 +97: =>start test 2 WHIM custom +97: [12:10:28] test on : 365 molecules done +118: [12:10:28] Rep: 0 Mol:29 +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +124: [12:10:28] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +124: [12:10:28] UFFTYPER: Unrecognized atom type: N_5 (2) +124: [12:10:28] UFFTYPER: Unrecognized atom type: N_5 (3) +124: [12:10:28] UFFTYPER: Unrecognized atom type: N_5 (2) +124: [12:10:28] UFFTYPER: Unrecognized atom type: N_5 (3) +118: [12:10:28] Rep: 0 Mol:14 +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +124: [12:10:28] UFFTYPER: Unrecognized charge state for atom: 1 +118: [12:10:28] Rep: 0 Mol:18 +124: [12:10:28] UFFTYPER: Unrecognized charge state for atom: 1 +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[12:10:28] UFFTYPER: Unrecognized hybridization for atom: 0 +122: [12:10:28] UFFTYPER: Unrecognized atom type: Cu+1 (0) +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: ..[12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:28] Rep: 0 Mol:22 +124: [12:10:28] UFFTYPER: Unrecognized charge state for atom: 1 +58: [12:10:28] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +58: [12:10:28] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +122: [12:10:28] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:28] Rep: 0 Mol:26 +118: [12:10:28] Rep: 0 Mol:30 122: ... 122: ---------------------------------------------------------------------- -122: Ran 18 tests in 0.444s +122: Ran 18 tests in 0.520s 122: 122: OK -124: [03:04:21] UFFTYPER: Unrecognized atom type: N_5 (2) -124: [03:04:21] UFFTYPER: Unrecognized atom type: N_5 (3) -118: [03:04:21] Rep: 0 Mol:1[03:04:21] Rep: 0 Mol:3 -118: -118: [03:04:21] Rep: 0 Mol:2 -118: [03:04:21] Rep: 0 Mol:5 -118: [03:04:21] Rep: 0 Mol:4 -118: [03:04:21] Rep: 0 Mol:9 -124: [03:04:21] UFFTYPER: Unrecognized charge state for atom: 1 -118: [03:04:21] Rep: 0 Mol:13 -124: [03:04:21] UFFTYPER: Unrecognized charge state for atom: 1 -118: [03:04:21] Rep: 0 Mol:8 -111/208 Test #122: pyForceFieldHelpers .................... Passed 1.16 sec +58: [12:10:28] Empty atom list: 'M ALS 1 0 F' on line 8. +58: de_DE.UTF-8 +58: [12:10:28] ------------------------------------- +58: [12:10:28] Test multithreading Locale Switching +118: [12:10:28] Rep: 20 Mol:0 +118: [12:10:28] Rep: 20 Mol:4 +118: [12:10:28] Rep: 20 Mol:8 +118: [12:10:28] Rep: 20 Mol:12 +118: [12:10:28] Rep: 20 Mol:16 +118: [12:10:28] Rep: 20 Mol:20 +118: [12:10:28] Rep: 20 Mol:24 +118: [12:10:28] Rep: 20 Mol:28 +120: processing +120: launch :0 +120: launch :1 +120: launch :2 +120: [12:10:28] Rep: 0 Mol: launch :3 +120: 1 +120: [12:10:28] Rep: 0 Mol:0 +120: [12:10:28] Rep: 0 Mol:5 +120: [12:10:28] Rep: 0 Mol:3 +120: [12:10:28] Rep: 0 Mol:2 +118: [12:10:28] Rep: 20 Mol:3 +118: [12:10:28] Rep: 20 Mol:7 +120: [12:10:28] Rep: 0 Mol:4 +118: [12:10:28] Rep: 20 Mol:11 +118: [12:10:28] Rep: 20 Mol:15 +118: [12:10:28] Rep: 20 Mol:19 +118: [12:10:28] Rep: 20 Mol:23 +118: [12:10:28] Rep: 20 Mol:27 +118: [12:10:28] Rep: 20 Mol:31 +120: [12:10:28] Rep: 0 Mol:9 +110/208 Test #122: pyForceFieldHelpers .................... Passed 1.34 sec test 126 Start 126: testMolAlign 126: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 126: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign 126: Test timeout computed to be: 1500 -118: [03:04:21] Rep: 0 Mol:12 -118: [03:04:21] Rep: 0 Mol:17 -124: [03:04:21] UFFTYPER: Unrecognized charge state for atom: 1 -118: [03:04:21] Rep: 0 Mol:6 -118: [03:04:21] Rep: 0 Mol:16 -118: [03:04:21] Rep: 0 Mol:10 -61: [03:04:21] Finished: testSmiCorrectness() -61: [03:04:21] ----------------------------------------- +120: [12:10:29] Rep: 0 Mol:13 +120: [12:10:29] Rep: 0 Mol:8 +125: .[12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:29] Rep: 0 Mol:7 +118: [12:10:29] Rep: 20 Mol:1 +118: [12:10:29] Rep: 20 Mol:5 +118: [12:10:29] Rep: 20 Mol:9 +120: [12:10:29] Rep: 0 Mol:6 +58: [12:10:29] Test multithreading (Done) +58: [12:10:29] ------------------------------------- +120: [12:10:29] Rep: 0 Mol:12 +118: [12:10:29] Rep: 20 Mol:13 +118: [12:10:29] Rep: 20 Mol:17 +118: [12:10:29] Rep: 20 Mol:21 +120: [12:10:29] Rep: 0 Mol:16 +120: [12:10:29] Rep: 0 Mol:11 +120: [12:10:29] Rep: 0 Mol:17 +124: [12:10:29] UFFTYPER: Unrecognized charge state for atom: 5 +118: [12:10:29] Rep: 20 Mol:25 +118: [12:10:29] Rep: 20 Mol:29 +120: [12:10:29] Rep: 0 Mol:10 +120: [12:10:29] Rep: 0 Mol:15 +120: [12:10:29] Rep: 0 Mol:20 +11: .................. +11: ---------------------------------------------------------------------- +11: Ran 18 tests in 12.265s +11: +11: OK +120: [12:10:29] Rep: 0 Mol:19 +58: *************************************** +58: *************************************** +120: [12:10:29] Rep: 0 Mol:24 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +120: [12:10:29] Rep: 0 Mol:23 +120: [12:10:29] Rep: 0 Mol:27 +120: [12:10:29] Rep: 0 Mol:28 +97: =>start test 1 WHIM custom +97: [12:10:29] test on : 365 molecules done +124: [12:10:29] UFFTYPER: Unrecognized charge state for atom: 5 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: ..[12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:29] Rep: 0 Mol:31 +58: [12:10:29] bond with order 0 found on line 7. This is not part of the MDL specification. +58: [12:10:29] unrecognized query bond type, 9, found on line 7. Using an "any" query. +120: [12:10:29] Rep: 0 Mol:21 +124: [12:10:29] UFFTYPER: Unrecognized charge state for atom: 5 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:29] Rep: 0 Mol:25 +120: [12:10:29] Rep: 0 Mol:14 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: ..[12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:29] Rep: 0 Mol:29 +120: [12:10:29] Rep: 0 Mol:18 +58: [12:10:29] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +58: [12:10:29] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +58: [12:10:29] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:29] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:29] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:29] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:29] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:29] Warning: molecule is tagged as 3D, but all Z coords are zero +125: .[12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +61: [12:10:29] Finished: testSmiCorrectness() +61: [12:10:29] ----------------------------------------- 61: -61: [03:04:21] +61: [12:10:29] 61: ----------------------------------------- -120: processing -120: launch :0 -120: launch :1 -120: launch :2 -120: launch :3 -120: [03:04:21] Rep: 0 Mol:1 -120: [03:04:21] Rep: 0 Mol:5 -120: [03:04:21] Rep: 0 Mol:9 -118: [03:04:21] Rep: 0 Mol:20 -120: [03:04:21] [03:04:21] Rep: 0 Mol:0 -118: [03:04:21] Rep: 0 Mol:7 -120: [03:04:21] Rep: 0 Mol:2 -120: Rep: 0 Mol:3 -118: [03:04:21] Rep: 0 Mol:11 -120: [03:04:21] Rep: 0 Mol:4 -118: [03:04:21] Rep: 0 Mol:24 -120: [03:04:21] Rep: 0 Mol:13 -118: [03:04:21] Rep: 0 Mol:15 -118: [03:04:21] Rep: 0 Mol:21 -118: [03:04:21] Rep: 0 Mol:19 -118: [03:04:21] Rep: 0 Mol:28 -118: [03:04:21] Rep: 0 Mol:23 -118: [03:04:21] Rep: 0 Mol:27 -118: [03:04:21] Rep: 0 Mol:25 -61: [03:04:21] Spurious data before the first property will be ignored -61: [03:04:21] Property will be truncated after the first blank line -61: [03:04:21] Property will be truncated after the first blank line -61: [03:04:21] Property will be truncated after the first blank line -120: [03:04:21] Rep: 0 Mol:17 -118: [03:04:21] Rep: 0 Mol:31 -120: [03:04:21] Rep: 0 Mol:7 -120: [03:04:21] Rep: 0 Mol:6 -120: [03:04:21] Rep: 0 Mol:8 -120: [03:04:21] Rep: 0 Mol:11 -118: [03:04:21] Rep: 0 Mol:29 -120: [03:04:21] Rep: 0[03:04:21] Rep: 0 Mol:10 -120: Mol:12 -120: [03:04:21] Rep: 0 Mol:15 -120: [03:04:21] Rep: 0 Mol:16 -120: [03:04:21] Rep: 0 Mol:19 -120: [03:04:21] Rep: 0 Mol:23 -120: [03:04:21] Rep: 0 Mol:20 -120: [03:04:21] Rep: 0 Mol:27 -120: [03:04:21] Rep: 0 Mol:31 -125: .[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -120: [03:04:21] Rep: 0 Mol:24 -120: [03:04:21] Rep: 0 Mol:21 -120: [03:04:21] Rep: 0 Mol:28 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: ..[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -120: [03:04:21] Rep: 0 Mol:25 -118: [03:04:21] Rep: 0 Mol:14 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: ..[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -120: [03:04:21] Rep: 0 Mol:14 -120: [03:04:21] Rep: 0 Mol:29 -125: .[03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -120: [03:04:21] Rep: 0 Mol:18 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -118: [03:04:21] Rep: 0 Mol:18 -118: [03:04:21] Rep: 20 Mol:3 -118: [03:04:21] Rep: 20 Mol:7 -118: [03:04:21] Rep: 20 Mol:11 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -118: [03:04:21] Rep: 20 Mol:15 -118: [03:04:21] Rep: 20 Mol:19 -118: [03:04:21] Rep: 20 Mol:23 -118: [03:04:21] Rep: 20 Mol:27 -118: [03:04:21] Rep: 20 Mol:31 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -120: [03:04:21] Rep: 0 Mol:22 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -120: [03:04:21] Rep: 0 Mol:26 -118: [03:04:21] Rep: 0 Mol:22 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:29] Rep: 0 Mol:22 +111/208 Test #11: pyBV ................................... Passed 13.39 sec +test 127 + Start 127: testO3AAlign + +127: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign +127: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign +127: Test timeout computed to be: 1500 +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 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:29] Rep: 0 Mol:26 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +58: check isomorphism +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:29] Rep: 0 Mol:30 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +61: [12:10:29] Spurious data before the first property will be ignored +61: [12:10:29] Property will be truncated after the first blank line +61: [12:10:29] Property will be truncated after the first blank line +61: [12:10:29] Property will be truncated after the first blank line +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:29] Rep: 40 Mol:1 +118: [12:10:29] Rep: 40 Mol:5 +118: [12:10:29] Rep: 40 Mol:9 +118: [12:10:29] Rep: 40 Mol:13 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:29] Rep: 40 Mol:17 +118: [12:10:29] Rep: 40 Mol:21 +118: [12:10:29] Rep: 40 Mol:25 +118: [12:10:29] Rep: 40 Mol:29 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:29] Rep: 40 Mol:3 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:29] Rep: 40 Mol:7 +118: [12:10:29] Rep: 40 Mol:11 +118: [12:10:29] Rep: 40 Mol:15 +118: [12:10:29] Rep: 40 Mol:19 +118: [12:10:29] Rep: 40 Mol:23 +118: [12:10:29] Rep: 40 Mol:27 +118: [12:10:29] Rep: 40 Mol:31 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:29] Rep: 20 Mol:2 +118: [12:10:29] Rep: 20 Mol:6 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:29] Rep: 20 Mol:10 +118: [12:10:29] Rep: 20 Mol:14 +118: [12:10:29] Rep: 20 Mol:18 +118: [12:10:29] Rep: 20 Mol:22 +118: [12:10:29] Rep: 20 Mol:26 +118: [12:10:29] Rep: 20 Mol:30 +118: [12:10:29] Rep: 40 Mol:0 +118: [12:10:29] Rep: 40 Mol:4 +118: [12:10:29] Rep: 40 Mol:8 +118: [12:10:29] Rep: 40 Mol:12 +118: [12:10:29] Rep: 40 Mol:16 +118: [12:10:29] Rep: 40 Mol:20 +118: [12:10:29] Rep: 40 Mol:24 +118: [12:10:29] Rep: 40 Mol:28 +25: All 191 tests passed +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +112/208 Test #39: resMolSupplierTest ..................... Passed 12.60 sec +test 128 + Start 128: molAlignCatchTest + +128: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest +128: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign +128: Test timeout computed to be: 1500 126: *********************************************************** 126: Testing MolAlign 126: --------------------------------- @@ -23883,220 +23991,81 @@ 126: testIssue241 126: 126: *********************************************************** -112/208 Test #126: testMolAlign ........................... Passed 0.35 sec -test 127 - Start 127: testO3AAlign - -127: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign -127: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign -127: Test timeout computed to be: 1500 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -120: [03:04:21] Rep: 0 Mol:30 -118: [03:04:21] Rep: 0 Mol:26 -124: [03:04:21] UFFTYPER: Unrecognized charge state for atom: 5 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -102: =>start test GETAWAY -102: [03:04:21] test on : 365 molecules done -113/208 Test #102: testGETAWAY ............................ Passed 4.74 sec -test 128 - Start 128: molAlignCatchTest - -128: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest -128: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolAlign -128: Test timeout computed to be: 1500 -118: [03:04:21] Rep: 20 Mol:0 -118: [03:04:21] Rep: 20 Mol:4 -118: [03:04:21] Rep: 20 Mol:8 -118: [03:04:21] Rep: 20 Mol:12 -118: [03:04:21] Rep: 20 Mol:16 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -124: [03:04:21] UFFTYPER: Unrecognized charge state for atom: 5 -118: [03:04:21] Rep: 0 Mol:30 -118: [03:04:21] Rep: 20 Mol:20 -118: [03:04:21] Rep: 20 Mol:24 -118: [03:04:21] Rep: 20 Mol:28 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -124: [03:04:21] UFFTYPER: Unrecognized charge state for atom: 5 -128: =============================================================================== -128: All tests passed (9 assertions in 1 test case) -128: -118: [03:04:21] Rep: 40 Mol:3 -118: [03:04:21] Rep: 40 Mol:7 -118: [03:04:21] Rep: 40 Mol:11 -118: [03:04:21] Rep: 40 Mol:15 -118: [03:04:21] Rep: 40 Mol:19 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -114/208 Test #128: molAlignCatchTest ...................... Passed 0.08 sec +124: [12:10:29] UFFTYPER: Unrecognized charge state for atom: 6 +113/208 Test #126: testMolAlign ........................... Passed 0.62 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-x86_64-linux-gnu/Code/GraphMol/MolAlign/Wrap 129: Test timeout computed to be: 1500 -118: [03:04:21] Rep: 40 Mol:23 -118: [03:04:21] Rep: 40 Mol:27 -118: [03:04:21] Rep: 40 Mol:31 -118: [03:04:21] Rep: 20 Mol:1 -118: [03:04:21] Rep: 20 Mol:5 -118: [03:04:21] Rep: 20 Mol:9 -118: [03:04:21] Rep: 20 Mol:13 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -118: [03:04:21] Rep: 20 Mol:17 -118: [03:04:21] Rep: 20 Mol:21 -118: [03:04:21] Rep: 20 Mol:25 -118: [03:04:21] Rep: 20 Mol:29 -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:21] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:22] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:22] Molecule does not have explicit Hs. Consider calling AddHs() -118: [03:04:22] Rep: 60 Mol:3 -118: [03:04:22] Rep: 60 Mol:7 -118: [03:04:22] Rep: 60 Mol:11 -118: [03:04:22] Rep: 60 Mol:15 -118: [03:04:22] Rep: 60 Mol:19 -118: [03:04:22] Rep: 60 Mol:23 -118: [03:04:22] Rep: 60 Mol:27 -118: [03:04:22] Rep: 60 Mol:31 -125: [03:04:22] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:04:22] Molecule does not have explicit Hs. Consider calling AddHs() -124: [03:04:22] UFFTYPER: Unrecognized charge state for atom: 6 -118: [03:04:22] Rep: 40 Mol:0 -125: [03:04:22] Molecule does not have explicit Hs. Consider calling AddHs() -118: [03:04:22] Rep: 40 Mol:4 -118: [03:04:22] Rep: 40 Mol:8 -118: [03:04:22] Rep: 40 Mol:12 -118: [03:04:22] Rep: 40 Mol:16 -118: [03:04:22] Rep: 40 Mol:20 -118: [03:04:22] Rep: 40 Mol:24 -118: [03:04:22] Rep: 40 Mol:28 -125: .[03:04:22] Molecule does not have explicit Hs. Consider calling AddHs() -124: [03:04:22] UFFTYPER: Unrecognized charge state for atom: 6 -124: [03:04:22] UFFTYPER: Unrecognized charge state for atom: 6 -118: [03:04:22] Rep: 20 Mol:2 -118: [03:04:22] Rep: 20 Mol:6 -118: [03:04:22] Rep: 20 Mol:10 -118: [03:04:22] Rep: 20 Mol:14 -118: [03:04:22] Rep: 20 Mol:18 -118: [03:04:22] Rep: 20 Mol:22 -118: [03:04:22] Rep: 40 Mol:1 -118: [03:04:22] Rep: 40 Mol:5 -118: [03:04:22] Rep: 40 Mol:9 -118: [03:04:22] Rep: 40 Mol:13 -118: [03:04:22] Rep: 40 Mol:17 -118: [03:04:22] Rep: 40 Mol:21 -118: [03:04:22] Rep: 40 Mol:25 -118: [03:04:22] Rep: 40 Mol:29 -118: [03:04:22] Rep: 20 Mol:26 -118: [03:04:22] Rep: 20 Mol:30 -125: [03:04:22] Molecule does not have explicit Hs. Consider calling AddHs() -118: [03:04:22] Rep: 80 Mol:3 -118: [03:04:22] Rep: 80 Mol:7 -118: [03:04:22] Rep: 80 Mol:11 -118: [03:04:22] Rep: 80 Mol:15 -118: [03:04:22] Rep: 80 Mol:19 -118: [03:04:22] Rep: 80 Mol:23 -118: [03:04:22] Rep: 80 Mol:27 -118: [03:04:22] Rep: 80 Mol:31 -120: [03:04:22] Rep: 100 Mol:0 -120: [03:04:22] Rep: 100 Mol:4 -120: [03:04:22] Rep: 100 Mol:8 -120: [03:04:22] Rep: 100 Mol:12 -120: [03:04:22] Rep: 100 Mol:16 -120: [03:04:22] Rep: 100 Mol:20 -120: [03:04:22] Rep: 100 Mol:24 -120: [03:04:22] Rep: 100 Mol:28 -120: [03:04:22] Rep: 100 Mol:3 -120: [03:04:22] Rep: 100 Mol:7 -120: [03:04:22] Rep: 100 Mol:11 -120: [03:04:22] Rep: 100 Mol:15 -120: [03:04:22] Rep: 100 Mol:19 -120: [03:04:22] Rep: 100 Mol:23 -120: [03:04:22] Rep: 100 Mol:27 -120: [03:04:22] Rep: 100 Mol:31 -118: [03:04:22] Rep: 60 Mol:0 -118: [03:04:22] Rep: 60 Mol:4 -118: [03:04:22] Rep: 60 Mol:8 -118: [03:04:22] Rep: 60 Mol:12 -118: [03:04:22] Rep: 60 Mol:16 -118: [03:04:22] Rep: 60 Mol:20 -118: [03:04:22] Rep: 60 Mol:24 -118: [03:04:22] Rep: 60 Mol:28 -120: [03:04:22] Rep: 100 Mol:1 -120: [03:04:22] Rep: 100 Mol:5 -120: [03:04:22] Rep: 100 Mol:9 -120: [03:04:22] Rep: 100 Mol:13 -120: [03:04:22] Rep: 100 Mol:17 -120: [03:04:22] Rep: 100 Mol:21 -120: [03:04:22] Rep: 100 Mol:25 -120: [03:04:22] Rep: 100 Mol:29 -61: [03:04:22] Finished: testSDCorrectness() -61: [03:04:22] ----------------------------------------- -61: -115/208 Test #61: testMultithreadedMolSupplier ........... Passed 10.46 sec +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +124: [12:10:29] UFFTYPER: Unrecognized charge state for atom: 6 +128: =============================================================================== +128: All tests passed (9 assertions in 1 test case) +128: +124: [12:10:29] UFFTYPER: Unrecognized charge state for atom: 6 +114/208 Test #128: molAlignCatchTest ...................... Passed 0.09 sec test 130 Start 130: testFeatures 130: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 130: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures 130: Test timeout computed to be: 1500 -130: [03:04:22] ------------------------------------- -130: [03:04:22] AtomType parser testing. -130: [03:04:22] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -130: [03:04:22] 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: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] FeatureDefinition parser testing. -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Test pulling feat defs from a string. -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] FeatureDef functionality testing. -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] FeatureFactory testing. -130: [03:04:22] 1 -130: [03:04:22] 2 -130: [03:04:22] 3 -130: [03:04:22] 4 -130: [03:04:22] 5 -130: [03:04:22] 6 -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Feature Location testing. -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Test building a FeatureFactory from a file -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Testing Issue 224. -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Testing Issue 225. -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Test Issue346 -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Test Issue347 -130: [03:04:22] done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Testing Issue 348. -130: [03:04:22] SMARTS Parse Error: syntax error while parsing: [C[C] -130: [03:04:22] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -130: [03:04:22] ------------------------------------- -130: [03:04:22] Testing Nested AtomType definitions. +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +130: [12:10:29] ------------------------------------- +130: [12:10:29] AtomType parser testing. +130: [12:10:29] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +130: [12:10:29] 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: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] FeatureDefinition parser testing. +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Test pulling feat defs from a string. +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] FeatureDef functionality testing. +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] FeatureFactory testing. +130: [12:10:29] 1 +130: [12:10:29] 2 +130: [12:10:29] 3 +130: [12:10:29] 4 +130: [12:10:29] 5 +130: [12:10:29] 6 +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Feature Location testing. +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Test building a FeatureFactory from a file +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Testing Issue 224. +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Testing Issue 225. +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Test Issue346 +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Test Issue347 +130: [12:10:29] done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Testing Issue 348. +130: [12:10:29] SMARTS Parse Error: syntax error while parsing: [C[C] +130: [12:10:29] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +130: [12:10:29] ------------------------------------- +130: [12:10:29] Testing Nested AtomType definitions. 130: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -130: [03:04:22] ------------------------------------- -130: [03:04:22] Testing Github Issue #252: crash when calling getPos() with no conformer. -130: [03:04:22] expect a precondition failure message below -130: [03:04:22] +130: [12:10:29] ------------------------------------- +130: [12:10:29] Testing Github Issue #252: crash when calling getPos() with no conformer. +130: [12:10:29] expect a precondition failure message below +130: [12:10:29] 130: 130: **** 130: Pre-condition Violation @@ -24105,106 +24074,165 @@ 130: Failed Expression: dp_mol->getNumConformers() 130: **** 130: -130: [03:04:22] Done -130: [03:04:22] ------------------------------------- -130: [03:04:22] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -130: [03:04:22] done -116/208 Test #130: testFeatures ........................... Passed 0.06 sec +130: [12:10:29] Done +130: [12:10:29] ------------------------------------- +130: [12:10:29] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +130: [12:10:29] done +115/208 Test #130: testFeatures ........................... Passed 0.07 sec test 131 Start 131: pyChemicalFeatures 131: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 131: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 131: Test timeout computed to be: 1500 -118: [03:04:22] Rep: 60 Mol:1 -118: [03:04:22] Rep: 60 Mol:5 -118: [03:04:22] Rep: 60 Mol:9 -118: [03:04:22] Rep: 60 Mol:13 -118: [03:04:22] Rep: 60 Mol:17 -118: [03:04:22] Rep: 60 Mol:21 -118: [03:04:22] Rep: 60 Mol:25 -118: [03:04:22] Rep: 60 Mol:29 -125: [03:04:22] Molecule does not have explicit Hs. Consider calling AddHs() -118: [03:04:22] Rep: 40 Mol:2 -118: [03:04:22] Rep: 40 Mol:6 -118: [03:04:22] Rep: 40 Mol:10 -118: [03:04:22] Rep: 40 Mol:14 -118: [03:04:22] Rep: 40 Mol:18 -118: [03:04:22] Rep: 40 Mol:22 -118: [03:04:22] Rep: 40 Mol:26 -118: [03:04:22] Rep: 40 Mol:30 -118: [03:04:22] Rep: 80 Mol:0 -118: [03:04:22] Rep: 80 Mol:4 -118: [03:04:22] Rep: 80 Mol:8 -118: [03:04:22] Rep: 80 Mol:12 -118: [03:04:22] Rep: 80 Mol:16 -118: [03:04:22] Rep: 80 Mol:20 -118: [03:04:22] Rep: 80 Mol:24 -118: [03:04:22] Rep: 80 Mol:28 -118: [03:04:23] Rep: 80 Mol:1 -118: [03:04:23] Rep: 80 Mol:5 -118: [03:04:23] Rep: 80 Mol:9 -118: [03:04:23] Rep: 80 Mol:13 -118: [03:04:23] Rep: 80 Mol:17 -118: [03:04:23] Rep: 80 Mol:21 -118: [03:04:23] Rep: 80 Mol:25 -118: [03:04:23] Rep: 80 Mol:29 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:29] Rep: 60 Mol:1 +118: [12:10:29] Rep: 60 Mol:5 +118: [12:10:29] Rep: 60 Mol:9 +118: [12:10:29] Rep: 60 Mol:13 +118: [12:10:29] Rep: 60 Mol:17 +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +118: [12:10:29] Rep: 60 Mol:21 +118: [12:10:29] Rep: 60 Mol:25 +118: [12:10:29] Rep: 60 Mol:29 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:29] Rep: 60 Mol:0 +118: [12:10:29] Rep: 60 Mol:4 +118: [12:10:29] Rep: 60 Mol:8 +118: [12:10:29] Rep: 60 Mol:12 +118: [12:10:29] Rep: 60 Mol:16 +118: [12:10:29] Rep: 60 Mol:20 +118: [12:10:29] Rep: 60 Mol:24 +118: [12:10:29] Rep: 60 Mol:28 +125: [12:10:29] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:30] Rep: 60 Mol:3 +118: [12:10:30] Rep: 60 Mol:7 +118: [12:10:30] Rep: 60 Mol:11 +118: [12:10:30] Rep: 60 Mol:15 +118: [12:10:30] Rep: 60 Mol:19 +118: [12:10:30] Rep: 60 Mol:23 +118: [12:10:30] Rep: 60 Mol:27 +118: [12:10:30] Rep: 60 Mol:31 +118: [12:10:30] Rep: 40 Mol:2 +118: [12:10:30] Rep: 40 Mol:6 +118: [12:10:30] Rep: 40 Mol:10 +118: [12:10:30] Rep: 40 Mol:14 +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:30] Rep: 40 Mol:18 +118: [12:10:30] Rep: 40 Mol:22 +118: [12:10:30] Rep: 40 Mol:26 +118: [12:10:30] Rep: 40 Mol:30 +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:30] Rep: 80 Mol:0 +118: [12:10:30] Rep: 80 Mol:4 +118: [12:10:30] Rep: 80 Mol:8 +118: [12:10:30] Rep: 80 Mol:12 +118: [12:10:30] Rep: 80 Mol:16 +118: [12:10:30] Rep: 80 Mol:20 +118: [12:10:30] Rep: 80 Mol:24 +118: [12:10:30] Rep: 80 Mol:28 +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:30] Rep: 100 Mol:0 +120: [12:10:30] Rep: 100 Mol:4 +120: [12:10:30] Rep: 100 Mol:8 +120: [12:10:30] Rep: 100 Mol:12 +120: [12:10:30] Rep: 100 Mol:16 +120: [12:10:30] Rep: 100 Mol:20 +120: [12:10:30] Rep: 100 Mol:24 +120: [12:10:30] Rep: 100 Mol:28 +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:30] Rep: 100 Mol:3 +120: [12:10:30] Rep: 100 Mol:7 +120: [12:10:30] Rep: 100 Mol:11 +120: [12:10:30] Rep: 100 Mol:15 +120: [12:10:30] Rep: 100 Mol:19 +120: [12:10:30] Rep: 100 Mol:23 +120: [12:10:30] Rep: 100 Mol:27 +120: [12:10:30] Rep: 100 Mol:31 +118: [12:10:30] Rep: 80 Mol:3 +118: [12:10:30] Rep: 80 Mol:7 +118: [12:10:30] Rep: 80 Mol:11 +118: [12:10:30] Rep: 80 Mol:15 +118: [12:10:30] Rep: 80 Mol:19 +118: [12:10:30] Rep: 80 Mol:23 +118: [12:10:30] Rep: 80 Mol:27 +118: [12:10:30] Rep: 80 Mol:31 +125: [12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:30] Rep: 80 Mol:1 +118: [12:10:30] Rep: 80 Mol:5 +118: [12:10:30] Rep: 80 Mol:9 +118: [12:10:30] Rep: 80 Mol:13 +118: [12:10:30] Rep: 80 Mol:17 +118: [12:10:30] Rep: 80 Mol:21 +118: [12:10:30] Rep: 80 Mol:25 +118: [12:10:30] Rep: 80 Mol:29 131: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:154: DeprecationWarning: Please use assertTrue instead. 131: self.failUnless(cfac.GetNumFeatureDefs() == 2) -58: [03:04:23] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [03:04:23] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [03:04:23] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [03:04:23] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [03:04:23] 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: [03:04:23] -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: +118: [12:10:30] Rep: 60 Mol:2 +118: [12:10:30] Rep: 60 Mol:6 +118: [12:10:30] Rep: 60 Mol:10 +118: [12:10:30] Rep: 60 Mol:14 +118: [12:10:30] Rep: 60 Mol:18 +118: [12:10:30] Rep: 60 Mol:22 +125: .[12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +118: [12:10:30] Rep: 60 Mol:26 +118: [12:10:30] Rep: 60 Mol:30 131: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:159: DeprecationWarning: Please use assertFalse instead. 131: self.failIf(m) -131: .[03:04:23] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:10:30] 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)) -118: [03:04:23] Rep: 60 Mol:2 -118: [03:04:23] Rep: 60 Mol:6 -118: [03:04:23] Rep: 60 Mol:10 -131: .[03:04:23] Molecule does not have explicit Hs. Consider calling AddHs() -118: [03:04:23] Rep: 60 Mol:14 -118: [03:04:23] Rep: 60 Mol:18 -118: [03:04:23] Rep: 60 Mol:22 -118: [03:04:23] Rep: 60 Mol:26 -118: [03:04:23] Rep: 60 Mol:30 -125: [03:04:23] Molecule does not have explicit Hs. Consider calling AddHs() -131: ..[03:04:23] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[03:04:23] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[03:04:23] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -131: [03:04:23] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +131: .[12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +131: ..[12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:10:30] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:10:30] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +131: [12:10:30] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 131: ... 131: ---------------------------------------------------------------------- -131: Ran 9 tests in 0.158s +131: Ran 9 tests in 0.222s 131: 131: OK -120: [03:04:23] Rep: 100 Mol:2 -120: [03:04:23] Rep: 100 Mol:6 -120: [03:04:23] Rep: 100 Mol:10 -120: [03:04:23] Rep: 100 Mol:14 -120: [03:04:23] Rep: 100 Mol:18 -120: [03:04:23] Rep: 100 Mol:22 -120: [03:04:23] Rep: 100 Mol:26 -120: [03:04:23] Rep: 100 Mol:30 -117/208 Test #131: pyChemicalFeatures ..................... Passed 0.73 sec +120: [12:10:30] Rep: 100 Mol:1 +120: [12:10:30] Rep: 100 Mol:5 +120: [12:10:30] Rep: 100 Mol:9 +120: [12:10:30] Rep: 100 Mol:13 +120: [12:10:30] Rep: 100 Mol:17 +120: [12:10:30] Rep: 100 Mol:21 +120: [12:10:30] Rep: 100 Mol:25 +120: [12:10:30] Rep: 100 Mol:29 +116/208 Test #131: pyChemicalFeatures ..................... Passed 1.07 sec test 132 Start 132: testShapeHelpers 132: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 132: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers 132: Test timeout computed to be: 1500 +61: [12:10:30] Finished: testSDCorrectness() +61: [12:10:30] ----------------------------------------- +61: +117/208 Test #61: testMultithreadedMolSupplier ........... Passed 13.19 sec +test 133 + Start 133: pyShapeHelpers + +133: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" +133: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap +133: Test timeout computed to be: 1500 +118: [12:10:30] Rep: 80 Mol:2 +118: [12:10:30] Rep: 80 Mol:6 +118: [12:10:30] Rep: 80 Mol:10 +118: [12:10:30] Rep: 80 Mol:14 +118: [12:10:30] Rep: 80 Mol:18 +118: [12:10:30] Rep: 80 Mol:22 +118: [12:10:30] Rep: 80 Mol:26 +118: [12:10:30] Rep: 80 Mol:30 132: *********************************************************** 132: Testing ShapeHelpers 132: --------------------------------- @@ -24218,62 +24246,57 @@ 132: 132: *********************************************************** 118/208 Test #132: testShapeHelpers ....................... Passed 0.10 sec -test 133 - Start 133: pyShapeHelpers - -133: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" -133: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap -133: Test timeout computed to be: 1500 -118: [03:04:23] Rep: 80 Mol:2 -118: [03:04:23] Rep: 80 Mol:6 -118: [03:04:23] Rep: 80 Mol:10 -118: [03:04:23] Rep: 80 Mol:14 -118: [03:04:23] Rep: 80 Mol:18 -118: [03:04:23] Rep: 80 Mol:22 -118: [03:04:23] Rep: 80 Mol:26 -118: [03:04:23] Rep: 80 Mol:30 -118: [03:04:23] done -118: [03:04:23] ------------------------------------- -118: [03:04:23] Test MMFF multithreading2 -125: [03:04:23] Molecule does not have explicit Hs. Consider calling AddHs() -133: . -133: ---------------------------------------------------------------------- -133: Ran 1 test in 0.228s -133: -133: OK -133: Testing Shape Helpers wrapper -125: [03:04:24] Molecule does not have explicit Hs. Consider calling AddHs() -119/208 Test #133: pyShapeHelpers ......................... Passed 1.11 sec test 134 Start 134: testMolCatalog 134: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 134: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog 134: Test timeout computed to be: 1500 -120/208 Test #134: testMolCatalog ......................... Passed 0.05 sec +119/208 Test #134: testMolCatalog ......................... Passed 0.06 sec test 135 Start 135: pyMolCatalog 135: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 135: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 135: Test timeout computed to be: 1500 -120: [03:04:24] done -120: [03:04:24] ------------------------------------- -120: [03:04:24] Test UFF multithreading2 -118: [03:04:24] done -118: [03:04:24] ------------------------------------- -118: [03:04:24] Test MMFF multithreading3 -97: =>start test GETAWAY custom -97: [03:04:25] test on : 365 molecules done -121/208 Test #97: testRDFcustom .......................... Passed 9.23 sec +125: [12:10:31] Molecule does not have explicit Hs. Consider calling AddHs() +120: [12:10:31] Rep: 100 Mol:2 +120: [12:10:31] Rep: 100 Mol:6 +120: [12:10:31] Rep: 100 Mol:10 +120: [12:10:31] Rep: 100 Mol:14 +120: [12:10:31] Rep: 100 Mol:18 +120: [12:10:31] Rep: 100 Mol:22 +120: [12:10:31] Rep: 100 Mol:26 +120: [12:10:31] Rep: 100 Mol:30 +118: [12:10:31] done +118: [12:10:31] ------------------------------------- +118: [12:10:31] Test MMFF multithreading2 +133: . +133: ---------------------------------------------------------------------- +133: Ran 1 test in 0.128s +133: +133: OK +133: Testing Shape Helpers wrapper +120/208 Test #133: pyShapeHelpers ......................... Passed 0.78 sec test 136 Start 136: moldraw2DTest1 136: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 136: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 136: Test timeout computed to be: 1500 -124: [03:04:25] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +135: . +135: ---------------------------------------------------------------------- +135: Ran 1 test in 0.042s +135: +135: OK 136: ----------------- Test 1 +121/208 Test #135: pyMolCatalog ........................... Passed 0.85 sec +test 137 + Start 137: moldraw2DTestCatch + +137: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +137: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D +137: Test timeout computed to be: 1500 136: file test1_5.svg gave hash 1886437816U not the expected 2964125114U 136: Done 136: ----------------- Test 2 @@ -24284,7 +24307,6 @@ 136: file test4_1.png gave hash 747479389U not the expected 1924202631U 136: Done 136: ----------------- Test 5 -124: [03:04:25] UFFTYPER: Warning: hybridization set to SP3 for atom 6 136: file test5_1.png gave hash 2840029290U not the expected 2116545562U 136: file test5_2.png gave hash 2160857868U not the expected 1519942634U 136: file test5_3.png gave hash 3012659882U not the expected 3266389887U @@ -24292,6 +24314,7 @@ 136: ----------------- Test 6 (atom labels) 136: Done 136: ----------------- Test 7 (backgrounds) +125: [12:10:32] Molecule does not have explicit Hs. Consider calling AddHs() 136: file test7_1.png gave hash 2457177866U not the expected 3331950391U 136: file test7_2.png gave hash 1086733527U not the expected 1686496331U 136: Done @@ -24299,94 +24322,134 @@ 136: Done 136: ----------------- Test multi-threaded drawing 136: reading molecules -124: [03:04:25] UFFTYPER: Warning: hybridization set to SP3 for atom 6 136: generating reference drawings -135: . -135: ---------------------------------------------------------------------- -135: Ran 1 test in 0.046s -135: -135: OK -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +120: [12:10:32] done +120: [12:10:32] ------------------------------------- +120: [12:10:32] Test UFF multithreading2 136: processing 136: launch :0 136: launch :1 136: launch :2 136: launch :3 -124: [03:04:25] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -124: [03:04:25] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -122/208 Test #135: pyMolCatalog ........................... Passed 1.20 sec -test 137 - Start 137: moldraw2DTestCatch - -137: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -137: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D -137: Test timeout computed to be: 1500 -124: [03:04:25] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: [12:10:32] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +58: [12:10:32] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [12:10:32] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [12:10:32] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [12:10:32] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [12:10:32] 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: [12:10:32] +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: +118: [12:10:32] done +118: [12:10:32] ------------------------------------- +118: [12:10:32] Test MMFF multithreading3 +124: [12:10:32] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +137: file testGithub3226_1.png gave hash 2749191424U not the expected 284815097U +124: [12:10:32] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +137: file testGithub3226_2.png gave hash 3002722972U not the expected 2460913971U +137: file testGithub3226_3.png gave hash 2190299399U not the expected 993799198U +137: file testPNGMetadata_1.png gave hash 602868208U not the expected 2022143293U +125: [12:10:33] Molecule does not have explicit Hs. Consider calling AddHs() +137: file testPNGMetadata_2.png gave hash 868131113U not the expected 3078435362U +124: [12:10:33] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: [12:10:33] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: [12:10:33] UFFTYPER: Warning: hybridization set to SP3 for atom 11 124: =============================================================================== 124: All tests passed (163 assertions in 5 test cases) 124: -25: All 191 tests passed -123/208 Test #124: distGeomHelpersCatch ................... Passed 5.46 sec +137: [12:10:33] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:33] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +122/208 Test #124: distGeomHelpersCatch ................... Passed 5.88 sec test 138 Start 138: moldraw2DRxnTest1 138: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 138: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolDraw2D 138: Test timeout computed to be: 1500 -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +137: file testHandDrawn-1.svg gave hash 4179827925U not the expected 799391905U +137: [12:10:33] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:33] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +123: building molecules +137: file testHandDrawn-1.png gave hash 925072819U not the expected 1551605661U 138: ----------------- Test 1 -138: file rxn_test1_1.png gave hash 410482668U not the expected 3579100589U -120: [03:04:26] done -120: [03:04:26] ------------------------------------- -120: [03:04:26] Test UFF multithreading3 -138: file rxn_test1_2.png gave hash 3429731987U not the expected 3996724834U -118: [03:04:26] done -118: [03:04:26] ------------------------------------- -118: [03:04:26] Testing github 162: Incorrect SMILES after MMFF parameterization . -118: [03:04:26] done -118: [03:04:26] ------------------------------------- -118: [03:04:26] Testing github 224: crash during MMFF parameterization . -118: [03:04:26] done -124/208 Test #118: testMMFFForceFieldHelpers .............. Passed 6.72 sec +118: [12:10:33] done +118: [12:10:33] ------------------------------------- +118: [12:10:33] Testing github 162: Incorrect SMILES after MMFF parameterization . +118: [12:10:33] done +118: [12:10:33] ------------------------------------- +118: [12:10:33] Testing github 224: crash during MMFF parameterization . +118: [12:10:33] done +123: generating reference data +123/208 Test #118: testMMFFForceFieldHelpers .............. Passed 7.44 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-x86_64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 139: Test timeout computed to be: 1500 +120: [12:10:33] done +120: [12:10:33] ------------------------------------- +120: [12:10:33] Test UFF multithreading3 +138: file rxn_test1_1.png gave hash 410482668U not the expected 3579100589U +137: [12:10:33] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:33] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +138: file rxn_test1_2.png gave hash 3429731987U not the expected 3996724834U +137: file testHandDrawn-2.svg gave hash 2499980011U not the expected 2605087576U +137: [12:10:34] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:34] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: file rxn_test1_3.png gave hash 645713784U not the expected 4153817948U +137: file testHandDrawn-2.png gave hash 2205473882U not the expected 2979412913U +137: [12:10:34] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:34] 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: [12:10:34] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:34] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: file rxn_test1_4.png gave hash 1948425776U not the expected 4175225545U +137: file testHandDrawn-3.png gave hash 1399046867U not the expected 1765396301U 138: file rxn_test1_5.png gave hash 918625681U not the expected 3400977230U +137: [12:10:34] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:34] 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: [12:10:34] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:34] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 138: file rxn_test1_6.png gave hash 203208251U not the expected 2636974466U +137: file testHandDrawn-4.png gave hash 462600014U not the expected 2989933219U 138: file rxn_test1_7.png gave hash 3679411321U not the expected 4164917700U 138: Done 138: ----------------- Test 2: some examples that caused problems in testing +125: [12:10:34] Molecule does not have explicit Hs. Consider calling AddHs() 138: file rxn_test2_1.png gave hash 2789407966U not the expected 2654417911U -137: file testGithub3226_1.png gave hash 2749191424U not the expected 284815097U +97: =>start test GETAWAY custom +97: [12:10:34] test on : 365 molecules done 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 -137: file testGithub3226_2.png gave hash 3002722972U not the expected 2460913971U +124/208 Test #97: testRDFcustom .......................... Passed 12.51 sec +test 140 + Start 140: testFMCS + +140: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS +140: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS +140: Test timeout computed to be: 1500 138: file rxn_test2_2_1.png gave hash 2636323184U 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 -137: file testGithub3226_3.png gave hash 2190299399U not the expected 993799198U -137: file testPNGMetadata_1.png gave hash 602868208U not the expected 2022143293U 138: file rxn_test2_2_2.png gave hash 3205071265U not the expected 2090979640U 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 138: file rxn_test2_2_3.png gave hash 3292764551U 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 -137: file testPNGMetadata_2.png gave hash 868131113U not the expected 3078435362U 138: file rxn_test2_2_4.png gave hash 2890404885U not the expected 610638635U 138: Done 138: ----------------- Test 3: test reactant highlighting -139: ...[03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -139: [03:04:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -138: file rxn_test3_1.png gave hash 3687422917U not the expected 501226401U -138: Done -138: ----------------- Test 4: some examples from SMARTS in testing -138: draw! -139: ..........[03:04:27] +139: ...[12:10:34] Font file /build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +139: [12:10:34] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +139: ..........[12:10:34] 139: 139: **** 139: Pre-condition Violation @@ -24395,95 +24458,50 @@ 139: Failed Expression: m 139: **** 139: -137: [03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:27] 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: [03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +138: file rxn_test3_1.png gave hash 3687422917U not the expected 501226401U +138: Done +138: ----------------- Test 4: some examples from SMARTS in testing +138: draw! 138: file rxn_test4_1.png gave hash 2224588892U not the expected 805353504U -137: file testHandDrawn-1.png gave hash 925072819U not the expected 1551605661U 138: file rxn_test4_1.svg gave hash 3996872002U not the expected 1987969092U 138: done -137: [03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:27] 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: [03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -137: file testHandDrawn-2.png gave hash 2205473882U not the expected 2979412913U -137: [03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:27] 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: [03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -137: file testHandDrawn-3.png gave hash 1399046867U not the expected 1765396301U -138: file rxn_test4_2.png gave hash 2983326139U not the expected 2842629749U -137: [03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:27] 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: [03:04:27] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:27] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -137: file testHandDrawn-4.png gave hash 462600014U not the expected 2989933219U -125: [03:04:27] Molecule does not have explicit Hs. Consider calling AddHs() -138: file rxn_test4_2.svg gave hash 3175821457U not the expected 946039978U -138: Done -120: [03:04:27] done -120: [03:04:27] ------------------------------------- -120: [03:04:27] Testing GitHubIssue62. -120: [03:04:27] beta-lactam 39.6387 -125/208 Test #138: moldraw2DRxnTest1 ...................... Passed 1.48 sec -test 140 - Start 140: testFMCS - -140: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/testFMCS -140: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS -140: Test timeout computed to be: 1500 -120: [03:04:27] cyclopropanone 174.698 -120: [03:04:27] aziridine 337.986 -120: [03:04:27] aziridinone 115.248 -120: [03:04:27] isobutene 2.48217 -120: [03:04:27] acetone 1.91788 -120: [03:04:27] cyclopentanone 10.1648 -120: [03:04:27] cyclopropene 99.4921 -120: [03:04:27] cyclobutene 41.0156 -120: [03:04:27] cyclopropane 267.236 -120: [03:04:27] gamma-lactam 15.7471 -123: building molecules -123: generating reference data -120: [03:04:27] trans-2,3-diphenylcyclopropan-1-one 203.398 -120: [03:04:27] cis-2,3-diphenylcyclopropan-1-one 206.852 139: ................... 139: ---------------------------------------------------------------------- -139: Ran 32 tests in 0.661s +139: Ran 32 tests in 0.347s 139: 139: OK -120: [03:04:27] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -120: [03:04:27] cyclopropylidencyclobutane 218.879 -120: [03:04:27] diphenylmethylidencyclobutane 79.6139 -120: [03:04:27] done -120: [03:04:27] ------------------------------------- -120: [03:04:27] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -120: [03:04:27] done -120: [03:04:27] ------------------------------------- -120: [03:04:27] Test square planar complexes -120: [03:04:27] done -120: [03:04:27] ------------------------------------- -120: [03:04:27] Test octahedral complexes -120: [03:04:27] done -125: [03:04:27] Molecule does not have explicit Hs. Consider calling AddHs() -126/208 Test #120: testUFFForceFieldHelpers ............... Passed 8.08 sec +138: file rxn_test4_2.png gave hash 2983326139U not the expected 2842629749U +120: [12:10:35] done +120: [12:10:35] ------------------------------------- +120: [12:10:35] Testing GitHubIssue62. +120: [12:10:35] beta-lactam 39.6387 +120: [12:10:35] cyclopropanone 174.698 +120: [12:10:35] aziridine 337.986 +120: [12:10:35] aziridinone 115.248 +120: [12:10:35] isobutene 2.48217 +120: [12:10:35] acetone 1.91788 +138: file rxn_test4_2.svg gave hash 3175821457U not the expected 946039978U +138: Done +120: [12:10:35] cyclopentanone 10.1648 +120: [12:10:35] cyclopropene 99.4921 +125/208 Test #138: moldraw2DRxnTest1 ...................... Passed 1.46 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-x86_64-linux-gnu/Code/GraphMol/FMCS/Wrap 141: Test timeout computed to be: 1500 -127/208 Test #139: pyMolDraw2D ............................ Passed 1.57 sec +120: [12:10:35] cyclobutene 41.0156 +120: [12:10:35] cyclopropane 267.236 +126/208 Test #139: pyMolDraw2D ............................ Passed 1.36 sec test 142 Start 142: FMCStest 142: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 142: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/FMCS/Test 142: Test timeout computed to be: 1500 +120: [12:10:35] gamma-lactam 15.7471 +125: [12:10:35] Molecule does not have explicit Hs. Consider calling AddHs() 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory 142: fopen testChEMBL_Txt(): No such file or directory @@ -26449,7 +26467,8 @@ 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 142: ERROR: RDKit could not load input file -128/208 Test #142: FMCStest ............................... Passed 0.10 sec +120: [12:10:35] trans-2,3-diphenylcyclopropan-1-one 203.398 +127/208 Test #142: FMCStest ............................... Passed 0.18 sec test 143 Start 143: molHashCatchTest @@ -26459,52 +26478,28 @@ 143: =============================================================================== 143: All tests passed (60 assertions in 5 test cases) 143: -129/208 Test #143: molHashCatchTest ....................... Passed 0.10 sec +128/208 Test #143: molHashCatchTest ....................... Passed 0.04 sec test 144 Start 144: pyMolHash 144: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 144: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolHash/Wrap 144: Test timeout computed to be: 1500 -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -108: [03:04:28] Warning: molecule is tagged as 3D, but all Z coords are zero -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Test unfolded version of RDKFP -108: [03:04:28] ------------------------------------- -108: [03:04:28] Test bitinfo of RDKFP -108: [03:04:28] ------------------------------------- -108: [03:04:28] Single atoms setting radius 1 bits in Morgan fingerprints -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Github #879: Pattern fingerprint should set bits for single-atom fragments. -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Github #2115: BitInfo not complete for RDKFingerprint -108: [03:04:28] done -108: [03:04:28] ------------------------------------- -108: [03:04:28] Github #3723: Fingerprint crash for mols with Zero order bonds -130/208 Test #108: testFingerprints ....................... Passed 10.28 sec +120: [12:10:35] cis-2,3-diphenylcyclopropan-1-one 206.852 +120: [12:10:35] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +120: [12:10:35] cyclopropylidencyclobutane 218.879 +120: [12:10:35] diphenylmethylidencyclobutane 79.6139 +120: [12:10:35] done +120: [12:10:35] ------------------------------------- +120: [12:10:35] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +120: [12:10:35] done +120: [12:10:35] ------------------------------------- +120: [12:10:35] Test square planar complexes +120: [12:10:35] done +120: [12:10:35] ------------------------------------- +120: [12:10:35] Test octahedral complexes +120: [12:10:35] done +129/208 Test #120: testUFFForceFieldHelpers ............... Passed 8.32 sec test 145 Start 145: testMMPA @@ -26513,7 +26508,7 @@ 145: Test timeout computed to be: 1500 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -145: Time elapsed 0.004623 seconds +145: Time elapsed 0.008663 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 @@ -26554,7 +26549,7 @@ 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 0.003940 seconds +145: Time elapsed 0.007937 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 @@ -26596,7 +26591,7 @@ 145: ----------------------------------- 145: 145: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -145: Time elapsed 0.004261 seconds +145: Time elapsed 0.008441 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] @@ -26605,6 +26600,11 @@ 145: 3: PASSED. matchedRefRes = 6 145: 4: res= O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OC[*:2] 145: 4: PASSED. matchedRefRes = 13 +144: .. +144: ---------------------------------------------------------------------- +144: Ran 2 tests in 0.019s +144: +144: OK 145: 5: res= O=C(NCC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].O[*:2] 145: 5: PASSED. matchedRefRes = 12 145: 6: res= NULL,Cc1c([*:1])[n+](=O)c2ccccc2n1[O-].O=C(NCCO)[*:1] @@ -26636,7 +26636,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -145: Time elapsed 0.001107 seconds +145: Time elapsed 0.001091 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] @@ -26647,6 +26647,9 @@ 145: 4: PASSED. matchedRefRes = 4 145: 5: res= NULL,C1CN1[*:1].CC(C=O)[*:1] 145: 5: PASSED. matchedRefRes = 5 +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Test GitHub Issue 258: Bad pattern fingerprint for query molecule 145: 6: res= CC([*:1])[*:2],C1CN1[*:2].O=C[*:1] 145: 6: NOREF. Reference data NOT LISTED in test case. 145: 7: res= NULL,CC(N1CC1)[*:1].O=C[*:1] @@ -26658,7 +26661,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -145: Time elapsed 0.004287 seconds +145: Time elapsed 0.008587 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 @@ -26687,6 +26690,45 @@ 145: 13: NOREF. Reference data NOT LISTED in test case. 145: 14: res= [C:0]([*:1])([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:1].Cc1ccccc1NC(=O)[*:2] 145: 14: NOREF. Reference data NOT LISTED in test case. +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +108: [12:10:35] Warning: molecule is tagged as 3D, but all Z coords are zero +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Test unfolded version of RDKFP +108: [12:10:35] ------------------------------------- +108: [12:10:35] Test bitinfo of RDKFP +108: [12:10:35] ------------------------------------- +108: [12:10:35] Single atoms setting radius 1 bits in Morgan fingerprints +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Github #879: Pattern fingerprint should set bits for single-atom fragments. +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Github #2115: BitInfo not complete for RDKFingerprint +130/208 Test #144: pyMolHash .............................. Passed 0.49 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-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap +146: Test timeout computed to be: 1500 145: 15: res= C[C:0]([*:1])[*:2],C1CC[NH+]([*:2])C1.Cc1ccccc1NC(=O)[*:1] 145: 15: NOREF. Reference data NOT LISTED in test case. 145: 16: res= NULL,C[*:1].Cc1ccccc1NC(=O)[C:2]([NH+]1CCCC1)[*:1] @@ -26695,15 +26737,25 @@ 145: 17: NOREF. Reference data NOT LISTED in test case. 145: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 145: 18: NOREF. Reference data NOT LISTED in test case. +108: [12:10:35] done +108: [12:10:35] ------------------------------------- +108: [12:10:35] Github #3723: Fingerprint crash for mols with Zero order bonds 145: 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: 145: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -145: Time elapsed 0.004327 seconds +145: Time elapsed 0.004591 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. +131/208 Test #108: testFingerprints ....................... Passed 11.25 sec +test 147 + Start 147: testCIPLabeler + +147: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler +147: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler +147: Test timeout computed to be: 1500 145: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 145: 2: NOREF. Reference data NOT LISTED in test case. 145: 3: res= O=C(O[*:2])[*:1],OC(c1ccccc1)[*:1].c1ccc(C[*:2])cc1 @@ -26742,88 +26794,35 @@ 145: --- ALL PASSED --- 145: ----------------------------------- 145: 5 TEST CASES FAILED -131/208 Test #145: testMMPA ............................... Passed 0.13 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-x86_64-linux-gnu/Code/GraphMol/MMPA/Wrap -146: Test timeout computed to be: 1500 -125: [03:04:28] Molecule does not have explicit Hs. Consider calling AddHs() -137: file testHandDrawn-5a.svg gave hash 2884622705U not the expected 2845825621U -137: [03:04:28] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:28] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -144: .. -144: ---------------------------------------------------------------------- -144: Ran 2 tests in 0.031s -144: -144: OK -137: file testHandDrawn-5b.svg gave hash 398482570U not the expected 476521352U -137: [03:04:28] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [03:04:28] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -137: file testHandDrawn-5.png gave hash 2620401141U not the expected 1526220279U -137: file testBrackets-5a.svg gave hash 4068248321U not the expected 1388227932U -132/208 Test #144: pyMolHash .............................. Passed 0.81 sec -test 147 - Start 147: testCIPLabeler - -147: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler -147: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler -147: Test timeout computed to be: 1500 -125: [03:04:28] Molecule does not have explicit Hs. Consider calling AddHs() -137: file testPositionVariation-1b.svg gave hash 919690070U not the expected 2588110577U -137: file testQueryBonds-1c.svg gave hash 1784325271U not the expected 333519907U -147: [03:04:29] non kekulizable aromatic bond being treated as bond order 1 -147: [03:04:29] non kekulizable aromatic bond being treated as bond order 1 -147: [03:04:29] non kekulizable aromatic bond being treated as bond order 1 -147: [03:04:29] non kekulizable aromatic bond being treated as bond order 1 -147: [03:04:29] non kekulizable aromatic bond being treated as bond order 1 -147: [03:04:29] non kekulizable aromatic bond being treated as bond order 1 -147: =============================================================================== -147: All tests passed (5974 assertions in 12 test cases) -147: -133/208 Test #147: testCIPLabeler ......................... Passed 0.08 sec +132/208 Test #145: testMMPA ............................... Passed 0.34 sec test 148 Start 148: pyCIPLabelsWrapTest 148: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 148: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 148: Test timeout computed to be: 1500 -58: [03:04:29] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [03:04:29] Warning: molecule is tagged as 3D, but all Z coords are zero -137: [03:04:29] unrecognized bond typefile testGithub4238_1.png gave hash 1493533853U not the expected 458925131U -137: file testGithub4323_1.png gave hash 858273747U not the expected 3711520691U -58: ---------------------------------- -58: ---------------------------------- -58: [03:04:29] -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: [03:04:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -137: file testGithub4323_3.png gave hash 747920275U not the expected 2300228708U -137: [03:04:29] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -58: [03:04:29] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -58: [03:04:29] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -58: [03:04:29] Empty atom list: 'M ALS 1 0 F' on line 8. -134/208 Test #58: fileParsersTest1 ....................... Passed 17.52 sec +147: [12:10:36] non kekulizable aromatic bond being treated as bond order 1 +147: [12:10:36] non kekulizable aromatic bond being treated as bond order 1 +147: [12:10:36] non kekulizable aromatic bond being treated as bond order 1 +147: [12:10:36] non kekulizable aromatic bond being treated as bond order 1 +147: [12:10:36] non kekulizable aromatic bond being treated as bond order 1 +147: [12:10:36] non kekulizable aromatic bond being treated as bond order 1 +147: =============================================================================== +147: All tests passed (5974 assertions in 12 test cases) +147: +133/208 Test #147: testCIPLabeler ......................... Passed 0.07 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-x86_64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 149: Test timeout computed to be: 1500 -125: [03:04:29] Molecule does not have explicit Hs. Consider calling AddHs() 148: ... 148: ---------------------------------------------------------------------- -148: Ran 3 tests in 0.031s +148: Ran 3 tests in 0.029s 148: 148: OK -135/208 Test #148: pyCIPLabelsWrapTest .................... Passed 0.71 sec +134/208 Test #148: pyCIPLabelsWrapTest .................... Passed 0.80 sec test 150 Start 150: deprotectTest @@ -26833,98 +26832,27 @@ 150: =============================================================================== 150: All tests passed (111 assertions in 3 test cases) 150: -136/208 Test #150: deprotectTest .......................... Passed 0.19 sec +135/208 Test #150: deprotectTest .......................... Passed 0.13 sec test 151 Start 151: pyDeprotect 151: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rough_test.py" 151: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Deprotect/Wrap 151: Test timeout computed to be: 1500 -76: 0,0 0 -76: 0,1 0 -76: 1,0 0 -76: 1,1 0 -76: 2,0 0 -76: 2,1 0 -137/208 Test #76: testEnumeration ........................ Passed 17.15 sec -test 152 - Start 152: testReducedGraphs - -152: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs -152: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs -152: Test timeout computed to be: 1500 -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, 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, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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Passed 0.09 sec -test 153 - Start 153: pyReducedGraphs - -153: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" -153: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -153: Test timeout computed to be: 1500 -146: ......... -146: ---------------------------------------------------------------------- -146: Ran 9 tests in 1.489s -146: -146: OK -137: file testFlexiCanvas.2a.png gave hash 3596300350U not the expected 3618977786U -137: file testFlexiCanvas.2b.png gave hash 868015450U not the expected 2780757414U -139/208 Test #146: pyMMPA ................................. Passed 1.88 sec -test 154 - Start 154: trajectoryTest - -154: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest -154: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory -154: Test timeout computed to be: 1500 -125: [03:04:30] Molecule does not have explicit Hs. Consider calling AddHs() -137: file testGithub4764.sz1.svg gave hash 500301395U not the expected 493786705U -137: file testGithub4764.sz2.svg gave hash 1037722937U not the expected 2704253898U -137: file testGithub4764.sz3.svg gave hash 2007222117U not the expected 1328896014U -137: file testGithub4764.sz1.png gave hash 1323673067U not the expected 2320783268U -137: file testGithub4764.sz2.png gave hash 2779153084U not the expected 3297570843U -137: file testGithub4764.sz3.png gave hash 2362143699U not the expected 2178018272U -137: file testGithub_5269_1.svg gave hash 3635725957U not the expected 2368496794U -137: file testGithub_5269_2.svg gave hash 607835614U not the expected 567813292U -137: file github5383_1.png gave hash 3767909564U not the expected 2963331215U -137: file github5156_2.svg gave hash 1130781980U not the expected 2606649270U -137: file acs1996_1.png gave hash 4036198339U not the expected 2674458798U -137: file acs1996_2.png gave hash 3786285444U 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: [03:04:30] 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: -140/208 Test #137: moldraw2DTestCatch ..................... Passed 4.66 sec -test 155 - Start 155: substructLibraryTest - -155: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest -155: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary -155: Test timeout computed to be: 1500 -155: [03:04:30] ------------------------------------- -155: [03:04:30] Test1 +137: file testHandDrawn-5a.svg gave hash 2884622705U not the expected 2845825621U +137: [12:10:36] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:36] 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: [12:10:37] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [12:10:37] Falling back to original font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: file testHandDrawn-5.png gave hash 2620401141U 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: [12:10:37] unrecognized bond typefile testGithub4238_1.png gave hash 1493533853U not the expected 458925131U 151: ..... 151: ---------------------------------------------------------------------- -151: Ran 5 tests in 0.103s +151: Ran 5 tests in 0.052s 151: 151: OK 151: Testing tert-butyldimethylsilyl @@ -26977,168 +26905,160 @@ 151: Testing acetamide 151: Testing carbobenzyloxy 151: Testing Acetal/Ketal +137: file testGithub4323_1.png gave hash 858273747U not the expected 3711520691U +136/208 Test #151: pyDeprotect ............................ Passed 0.54 sec +test 152 + Start 152: testReducedGraphs + +152: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs +152: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs +152: Test timeout computed to be: 1500 +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, 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, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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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: +137/208 Test #152: testReducedGraphs ...................... Passed 0.10 sec +test 153 + Start 153: pyReducedGraphs + +153: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" +153: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +153: Test timeout computed to be: 1500 +137: file testGithub4323_3.png gave hash 747920275U not the expected 2300228708U +125: [12:10:37] Molecule does not have explicit Hs. Consider calling AddHs() +137: [12:10:37] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 153: ..... 153: ---------------------------------------------------------------------- -153: Ran 5 tests in 0.038s +153: Ran 5 tests in 0.035s 153: 153: OK -127: *********************************************************** -127: Testing O3AAlign -127: --------------------------------- -127: testMMFFO3A -127: -127: --------------------------------- -127: testMMFFO3A with pre-computed dmat and MolHistogram -127: -127: --------------------------------- -127: testMMFFO3A with constraints -127: -127: --------------------------------- -127: testMMFFO3A with variable weight constraints followed by local-only optimization -127: -127: --------------------------------- -127: testCrippenO3A -127: -127: --------------------------------- -127: testCrippenO3A with pre-computed dmat and MolHistogram -127: -127: --------------------------------- -127: testCrippenO3A with constraints -127: -127: --------------------------------- -127: testCrippenO3A with variable weight constraints followed by local-only optimization -127: -127: --------------------------------- -127: testMMFFO3A multithreading -127: -127: generating reference data -141/208 Test #151: pyDeprotect ............................ Passed 0.79 sec +138/208 Test #153: pyReducedGraphs ........................ Passed 0.70 sec +test 154 + Start 154: trajectoryTest + +154: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest +154: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Trajectory +154: Test timeout computed to be: 1500 +125: [12:10:38] Molecule does not have explicit Hs. Consider calling AddHs() +137: file testFlexiCanvas.2a.png gave hash 3596300350U not the expected 3618977786U +137: file testFlexiCanvas.2b.png gave hash 868015450U not the expected 2780757414U +137: file testGithub4764.sz1.svg gave hash 500301395U not the expected 493786705U +137: file testGithub4764.sz2.svg gave hash 1037722937U not the expected 2704253898U +137: file testGithub4764.sz3.svg gave hash 2007222117U not the expected 1328896014U +137: file testGithub4764.sz1.png gave hash 1323673067U not the expected 2320783268U +137: file testGithub4764.sz2.png gave hash 2779153084U not the expected 3297570843U +137: file testGithub4764.sz3.png gave hash 2362143699U not the expected 2178018272U +125: [12:10:38] Molecule does not have explicit Hs. Consider calling AddHs() +146: ......... +146: ---------------------------------------------------------------------- +146: Ran 9 tests in 2.715s +146: +146: OK +137: file testGithub_5269_1.svg gave hash 3635725957U not the expected 2368496794U +137: file testGithub_5269_2.svg gave hash 607835614U not the expected 567813292U +137: file github5383_1.png gave hash 3767909564U not the expected 2963331215U +137: file github5156_2.svg gave hash 1130781980U not the expected 2606649270U +137: file acs1996_1.png gave hash 4036198339U not the expected 2674458798U +139/208 Test #146: pyMMPA ................................. Passed 3.19 sec +test 155 + Start 155: substructLibraryTest + +155: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest +155: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary +155: Test timeout computed to be: 1500 +137: file acs1996_2.png gave hash 3786285444U not the expected 83755168U +140/208 Test #154: trajectoryTest ......................... Passed 0.88 sec test 156 Start 156: substructLibraryCatchTest 156: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 156: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary 156: Test timeout computed to be: 1500 -142/208 Test #153: pyReducedGraphs ........................ Passed 0.72 sec +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: [12:10:39] 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. +155: [12:10:39] ------------------------------------- +155: [12:10:39] Test1 +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: +141/208 Test #137: moldraw2DTestCatch ..................... Passed 7.39 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-x86_64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 157: Test timeout computed to be: 1500 -155: [03:04:30] done -155: [03:04:30] ------------------------------------- -155: [03:04:30] Test2 -143/208 Test #154: trajectoryTest ......................... Passed 0.69 sec +125: [12:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +155: [12:10:39] done +155: [12:10:39] ------------------------------------- +155: [12:10:39] Test2 +156: =============================================================================== +156: All tests passed (111 assertions in 4 test cases) +156: +142/208 Test #156: substructLibraryCatchTest .............. Passed 1.08 sec test 158 Start 158: testRGroupDecomp 158: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 158: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition 158: Test timeout computed to be: 1500 -155: [03:04:31] done -155: [03:04:31] ------------------------------------- -155: [03:04:31] Test3 (stereo options) -155: [03:04:31] Done (stereo options) -155: [03:04:31] ------------------------------------- -155: [03:04:31] Test4 (trusted smiles) -158: [03:04:31] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -156: =============================================================================== -156: All tests passed (111 assertions in 4 test cases) -156: -144/208 Test #156: substructLibraryCatchTest .............. Passed 0.82 sec -test 159 - Start 159: testRGroupDecompInternals - -159: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals -159: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -159: Test timeout computed to be: 1500 -158: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -155: [03:04:31] Done (trusted smiles) -155: [03:04:31] ------------------------------------- -155: [03:04:31] Testing C++ docs -155: [03:04:31] Done (C++ doc tests) -155: [03:04:31] ------------------------------------- -155: [03:04:31] Testing C++ ring query: PatternHolder -155: [03:04:31] Done (C++ ring query tests) -155: [03:04:31] ------------------------------------- -155: [03:04:31] Testing C++ ring query: TautomerPatternHolder -155: [03:04:31] Done (C++ ring query tests) -155: [03:04:31] ------------------------------------- -155: [03:04:31] Add Patterns -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [03:04:31] WARNING: not removing hydrogen atom with dummy atom neighbors -145/208 Test #159: testRGroupDecompInternals .............. Passed 0.09 sec -test 160 - Start 160: rgroupCatchTests - -160: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests -160: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition -160: Test timeout computed to be: 1500 -160: =============================================================================== -160: All tests passed (142 assertions in 10 test cases) -160: -146/208 Test #160: rgroupCatchTests ....................... Passed 0.42 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-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap -161: Test timeout computed to be: 1500 -123: validating reference data +125: [12:10:40] Molecule does not have explicit Hs. Consider calling AddHs() +155: [12:10:40] done +155: [12:10:40] ------------------------------------- +155: [12:10:40] Test3 (stereo options) +58: [12:10:40] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [12:10:40] Warning: molecule is tagged as 3D, but all Z coords are zero 140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 140: Time elapsed 0.000 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 0.196 seconds +140: Time elapsed 0.322 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 0.025 seconds +140: Time elapsed 0.053 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 0.041 seconds +140: Time elapsed 0.077 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 0.290 seconds +140: Time elapsed 0.369 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 0.288 seconds +140: Time elapsed 0.398 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 0.361 seconds +140: Time elapsed 0.424 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 0.372 seconds +140: Time elapsed 0.424 seconds 140: 140: testSegFault() 140: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.026 seconds +140: Time elapsed 0.029 seconds 140: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.032 seconds +140: Time elapsed 0.035 seconds 140: MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.039 seconds +140: Time elapsed 0.042 seconds 140: 140: testThreshold() 140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -27146,15 +27066,15 @@ 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 1.521 seconds +140: Time elapsed 1.680 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 0.867 seconds +140: Time elapsed 0.998 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 0.792 seconds +140: Time elapsed 0.816 seconds 140: 140: testAtomCompareIsotopes() 140: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -140: Time elapsed 0.004 seconds +140: Time elapsed 0.000 seconds 140: 140: testAtomCompareAnyAtom() 140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds @@ -27174,33 +27094,84 @@ 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 0.025 seconds +140: Time elapsed 0.028 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 -125: .[03:04:32] Molecule does not have explicit Hs. Consider calling AddHs() -127: processing -127: launch :0 -127: launch :1 -127: launch :2 -127: launch :3 -140: Time elapsed 0.002 seconds +155: [12:10:40] Done (stereo options) +155: [12:10:40] ------------------------------------- +155: [12:10:40] Test4 (trusted smiles) +58: ---------------------------------- +58: ---------------------------------- +58: [12:10:40] +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: [12:10:40] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +155: [12:10:40] Done (trusted smiles) +155: [12:10:40] ------------------------------------- +155: [12:10:40] Testing C++ docs +155: [12:10:40] Done (C++ doc tests) +155: [12:10:40] ------------------------------------- +155: [12:10:40] Testing C++ ring query: PatternHolder +155: [12:10:40] Done (C++ ring query tests) +155: [12:10:40] ------------------------------------- +155: [12:10:40] Testing C++ ring query: TautomerPatternHolder +155: [12:10:40] Done (C++ ring query tests) +155: [12:10:40] ------------------------------------- +155: [12:10:40] Add Patterns +127: *********************************************************** +127: Testing O3AAlign +127: --------------------------------- +127: testMMFFO3A +127: +127: --------------------------------- +127: testMMFFO3A with pre-computed dmat and MolHistogram +127: +127: --------------------------------- +127: testMMFFO3A with constraints +127: +127: --------------------------------- +127: testMMFFO3A with variable weight constraints followed by local-only optimization +127: +127: --------------------------------- +127: testCrippenO3A +127: +127: --------------------------------- +127: testCrippenO3A with pre-computed dmat and MolHistogram +127: +127: --------------------------------- +127: testCrippenO3A with constraints +127: +127: --------------------------------- +127: testCrippenO3A with variable weight constraints followed by local-only optimization +127: +127: --------------------------------- +127: testMMFFO3A multithreading +127: +127: generating reference data +140: Time elapsed 0.014 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 0.028 seconds +140: Time elapsed 0.019 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 0.354 seconds +140: Time elapsed 0.319 seconds 140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -140: Time elapsed 0.015 seconds +140: Time elapsed 0.003 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 0.107 seconds +140: Time elapsed 0.088 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 0.0179 seconds. bond[0]=6 +140: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0052 seconds. bond[0]=6 140: STATISTICS: -140: Total Growing Steps = 1, MCS found on 1 step, for 0.0179 seconds +140: Total Growing Steps = 1, MCS found on 1 step, for 0.0052 seconds 140: Initial Seeds = 1, Mismatched 0 140: Inspected Seeds = 2 140: Rejected by BestSize = 0 @@ -27219,7 +27190,7 @@ 140: HashFoundInCache= 0 140: ExactMatchCalls = 0 140: ExactMatchFound = 0 -140: Time elapsed 0.018 seconds +140: Time elapsed 0.006 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 @@ -27319,12 +27290,65 @@ 140: 140: MCS: [#6]-&!@[#6] 2 atoms, 1 bonds 140: -161: ............... -161: ---------------------------------------------------------------------- -161: Ran 15 tests in 2.745s -161: -161: OK -147/208 Test #161: pyRGroupDecomposition .................. Passed 3.47 sec +125: [12:10:41] Molecule does not have explicit Hs. Consider calling AddHs() +158: [12:10:41] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +158: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +76: 0,0 0 +76: 0,1 0 +76: 1,0 0 +76: 1,1 0 +76: 2,0 0 +76: 2,1 0 +143/208 Test #76: testEnumeration ........................ Passed 22.58 sec +test 159 + Start 159: testRGroupDecompInternals + +159: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals +159: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +159: Test timeout computed to be: 1500 +123: validating reference data +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [12:10:41] WARNING: not removing hydrogen atom with dummy atom neighbors +144/208 Test #159: testRGroupDecompInternals .............. Passed 0.09 sec +test 160 + Start 160: rgroupCatchTests + +160: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests +160: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition +160: Test timeout computed to be: 1500 +58: [12:10:41] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +58: [12:10:41] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +160: =============================================================================== +160: All tests passed (142 assertions in 10 test cases) +160: +145/208 Test #160: rgroupCatchTests ....................... Passed 0.41 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-x86_64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap +161: Test timeout computed to be: 1500 +58: [12:10:41] Empty atom list: 'M ALS 1 0 F' on line 8. +146/208 Test #58: fileParsersTest1 ....................... Passed 24.39 sec test 162 Start 162: molInterchangeTest1 @@ -27339,19 +27363,19 @@ 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]]}]}]} -148/208 Test #162: molInterchangeTest1 .................... Passed 0.08 sec +147/208 Test #162: molInterchangeTest1 .................... Passed 0.14 sec test 163 Start 163: molInterchangeCatchTest 163: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 163: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolInterchange 163: Test timeout computed to be: 1500 -163: [03:04:35] unrecognized bond type set to zero while writing -163: [03:04:35] unrecognized bond type set to zero while writing +163: [12:10:41] unrecognized bond type set to zero while writing +163: [12:10:41] unrecognized bond type set to zero while writing 163: =============================================================================== 163: All tests passed (14 assertions in 1 test case) 163: -149/208 Test #163: molInterchangeCatchTest ................ Passed 0.05 sec +148/208 Test #163: molInterchangeCatchTest ................ Passed 0.12 sec test 164 Start 164: pyMolInterchange @@ -27360,98 +27384,184 @@ 164: Test timeout computed to be: 1500 164: . 164: ---------------------------------------------------------------------- -164: Ran 1 test in 0.014s +164: Ran 1 test in 0.037s 164: 164: OK -150/208 Test #164: pyMolInterchange ....................... Passed 0.40 sec +149/208 Test #164: pyMolInterchange ....................... Passed 0.96 sec test 165 Start 165: testSLNParse 165: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 165: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse 165: Test timeout computed to be: 1500 -165: [03:04:36] SLN Parse Error: syntax error while parsing: CH4[I=13] -165: [03:04:36] Failed parsing SLN 'CH4[I=13]' -165: [03:04:36] SLN Parser error: Atom ID 1 appears *after* its ring closure. -165: [03:04:36] SLN Parser error: Ring closure 1 does not have a corresponding opener. -165: [03:04:36] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -165: [03:04:36] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -165: [03:04:36] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -165: [03:04:36] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -165: [03:04:36] SLN Parse Error: syntax error while parsing: CH4 fff -165: [03:04:36] Failed parsing SLN 'CH4 fff' -165: [03:04:36] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -165: [03:04:36] Failed parsing SLN 'C[charge=+1] foo' -165: [03:04:36] Query property 'is' ignored on non-query atom -165: [03:04:36] Query property 'is' ignored on non-query atom -151/208 Test #165: testSLNParse ........................... Passed 0.04 sec +165: [12:10:43] SLN Parse Error: syntax error while parsing: CH4[I=13] +165: [12:10:43] Failed parsing SLN 'CH4[I=13]' +165: [12:10:43] SLN Parser error: Atom ID 1 appears *after* its ring closure. +165: [12:10:43] SLN Parser error: Ring closure 1 does not have a corresponding opener. +165: [12:10:43] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +165: [12:10:43] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +165: [12:10:43] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +165: [12:10:43] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +165: [12:10:43] SLN Parse Error: syntax error while parsing: CH4 fff +165: [12:10:43] Failed parsing SLN 'CH4 fff' +165: [12:10:43] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +165: [12:10:43] Failed parsing SLN 'C[charge=+1] foo' +165: [12:10:43] Query property 'is' ignored on non-query atom +165: [12:10:43] Query property 'is' ignored on non-query atom +150/208 Test #165: testSLNParse ........................... Passed 0.06 sec test 166 Start 166: pySLNParse 166: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" 166: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/SLNParse/Wrap 166: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 166: /build/reproducible-path/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/testSLN.py:50: DeprecationWarning: Please use assertTrue instead. 166: self.failUnless(m1) 166: .. 166: ---------------------------------------------------------------------- -166: Ran 2 tests in 0.014s +166: Ran 2 tests in 0.018s 166: 166: OK -25: All 191 tests passed -152/208 Test #166: pySLNParse ............................. Passed 0.41 sec +151/208 Test #166: pySLNParse ............................. Passed 0.50 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-x86_64-linux-gnu/Code/GraphMol/Wrap 167: Test timeout computed to be: 1500 -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -140: [03:04:37] The provided InitialSeed is not an MCS and will be ignored +127: processing +127: launch :0 +127: launch :1 +127: launch :2 +127: launch :3 +125: .[12:10:44] Molecule does not have explicit Hs. Consider calling AddHs() +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +140: [12:10:44] 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 9.46 seconds -153/208 Test #140: testFMCS ............................... Passed 9.52 sec +140: TOTAL Time elapsed 10.48 seconds +152/208 Test #140: testFMCS ............................... Passed 10.55 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-x86_64-linux-gnu/Code/GraphMol/Wrap 168: Test timeout computed to be: 1500 -141: ...........................................[03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: [03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: [03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: .[03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: [03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: [03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: .[03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: [03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: [03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: .[03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: [03:04:37] The provided InitialSeed is not an MCS and will be ignored -141: [03:04:37] The provided InitialSeed is not an MCS and will be ignored -155: [03:04:37] ------------------------------------- -155: [03:04:37] testing PatternHolder -141: ................. -141: ---------------------------------------------------------------------- -141: Ran 63 tests in 8.935s -141: -141: OK -158: iterative -154/208 Test #141: pyFMCS ................................. Passed 9.39 sec +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +167: ..............[12:10:45] SMARTS Parse Error: syntax error while parsing: fiib +167: [12:10:45] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +167: ....[12:10:45] ERROR: Problems encountered parsing data fields +167: [12:10:45] ERROR: moving to the beginning of the next molecule +167: [12:10:45] ERROR: Problems encountered parsing data fields +167: [12:10:45] ERROR: moving to the beginning of the next molecule +167: [12:10:45] Spurious data before the first property will be ignored +167: [12:10:45] Property will be truncated after the first blank line +167: [12:10:45] Property will be truncated after the first blank line +167: [12:10:45] Property will be truncated after the first blank line +167: [12:10:45] ERROR: Problems encountered parsing data fields +167: [12:10:45] ERROR: moving to the beginning of the next molecule +167: [12:10:45] ERROR: Problems encountered parsing data fields +167: [12:10:45] ERROR: moving to the beginning of the next molecule +167: [12:10:45] Spurious data before the first property will be ignored +167: [12:10:45] Property will be truncated after the first blank line +167: [12:10:45] Property will be truncated after the first blank line +167: [12:10:45] Property will be truncated after the first blank line +167: [12:10:45] ERROR: Problems encountered parsing data fields +167: [12:10:45] ERROR: moving to the beginning of the next molecule +167: [12:10:45] Property will be truncated after the first blank line +167: [12:10:45] ERROR: Problems encountered parsing data fields +167: [12:10:45] ERROR: moving to the beginning of the next molecule +167: [12:10:45] Property will be truncated after the first blank line +167: .[12:10:45] SMILES Parse Error: syntax error while parsing: fail +167: [12:10:45] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +167: [12:10:45] ERROR: Smiles parse error on line 2 +167: [12:10:45] ERROR: Cannot create molecule from : 'fail' +167: >>> This may result in an infinite loop. It should finish almost instantly +167: <<< OK, it finished. +141: ...........................................[12:10:45] The provided InitialSeed is not an MCS and will be ignored +141: [12:10:45] The provided InitialSeed is not an MCS and will be ignored +141: [12:10:45] The provided InitialSeed is not an MCS and will be ignored +167: ............[12:10:45] Explicit valence for atom # 1 C, 5, is greater than permitted +141: .[12:10:45] The provided InitialSeed is not an MCS and will be ignored +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) +141: [12:10:45] The provided InitialSeed is not an MCS and will be ignored +167: ..[12:10:45] non-ring atom 0 marked aromatic +167: [12:10:45] non-ring atom 0 marked aromatic +167: [12:10:45] +167: +167: **** +167: Range Error +167: idx +167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +167: Failed Expression: 12 < 6 +167: **** +167: +167: [12:10:45] non-ring atom 0 marked aromatic +167: [12:10:45] non-ring atom 0 marked aromatic +167: [12:10:45] +167: +167: **** +167: Range Error +167: idx +167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +167: Failed Expression: 12 < 6 +167: **** +167: +141: [12:10:45] The provided InitialSeed is not an MCS and will be ignored +141: .[12:10:45] The provided InitialSeed is not an MCS and will be ignored +141: [12:10:45] The provided InitialSeed is not an MCS and will be ignored +141: [12:10:45] The provided InitialSeed is not an MCS and will be ignored +167: ...............[12:10:45] 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: [12:10:45] 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. +168: ...... +168: ---------------------------------------------------------------------- +168: Ran 6 tests in 0.039s +168: +168: OK +141: .[12:10:45] The provided InitialSeed is not an MCS and will be ignored +141: [12:10:45] The provided InitialSeed is not an MCS and will be ignored +141: [12:10:45] The provided InitialSeed is not an MCS and will be ignored +153/208 Test #168: pyTestConformerWrap .................... Passed 0.80 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-x86_64-linux-gnu/Code/GraphMol/Wrap 169: Test timeout computed to be: 1500 -169: [03:04:37] +167: ..............[12:10:45] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +167: [12:10:45] Explicit valence for atom # 1 C, 5, is greater than permitted +141: ................. +141: ---------------------------------------------------------------------- +141: Ran 63 tests in 10.227s +141: +141: OK +154/208 Test #141: pyFMCS ................................. Passed 11.02 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-x86_64-linux-gnu/Code/GraphMol/Wrap +170: Test timeout computed to be: 1500 +161: ............... +161: ---------------------------------------------------------------------- +161: Ran 15 tests in 3.953s +161: +161: OK +155/208 Test #161: pyRGroupDecomposition .................. Passed 4.85 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-x86_64-linux-gnu/Code/GraphMol/Wrap +171: Test timeout computed to be: 1500 +169: [12:10:46] 169: 169: **** 169: Pre-condition Violation @@ -27460,7 +27570,7 @@ 169: Failed Expression: from < static_cast(size()) 169: **** 169: -169: .[03:04:37] +169: .[12:10:46] 169: 169: **** 169: Pre-condition Violation @@ -27469,85 +27579,21 @@ 169: Failed Expression: from < static_cast(size()) 169: **** 169: -167: ..............[03:04:37] SMARTS Parse Error: syntax error while parsing: fiib -167: [03:04:37] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -155: [03:04:37] ------------------------------------- -155: [03:04:37] testing TautomerPatternHolder -167: ....[03:04:37] ERROR: Problems encountered parsing data fields -167: [03:04:37] ERROR: moving to the beginning of the next molecule -167: [03:04:37] ERROR: Problems encountered parsing data fields -167: [03:04:37] ERROR: moving to the beginning of the next molecule -167: [03:04:37] Spurious data before the first property will be ignored -167: [03:04:37] Property will be truncated after the first blank line -167: [03:04:37] Property will be truncated after the first blank line -167: [03:04:37] Property will be truncated after the first blank line -167: [03:04:37] ERROR: Problems encountered parsing data fields -167: [03:04:37] ERROR: moving to the beginning of the next molecule -167: [03:04:37] ERROR: Problems encountered parsing data fields -167: [03:04:37] ERROR: moving to the beginning of the next molecule -167: [03:04:37] Spurious data before the first property will be ignored -167: [03:04:37] Property will be truncated after the first blank line -167: [03:04:37] Property will be truncated after the first blank line -167: [03:04:37] Property will be truncated after the first blank line -167: [03:04:37] ERROR: Problems encountered parsing data fields -167: [03:04:37] ERROR: moving to the beginning of the next molecule -167: [03:04:37] Property will be truncated after the first blank line -167: [03:04:37] ERROR: Problems encountered parsing data fields -167: [03:04:37] ERROR: moving to the beginning of the next molecule -167: [03:04:37] Property will be truncated after the first blank line -168: ...... -168: ---------------------------------------------------------------------- -168: Ran 6 tests in 0.045s -168: -168: OK -167: .[03:04:37] SMILES Parse Error: syntax error while parsing: fail -167: [03:04:37] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -167: [03:04:37] ERROR: Smiles parse error on line 2 -167: [03:04:37] ERROR: Cannot create molecule from : 'fail' -167: >>> This may result in an infinite loop. It should finish almost instantly -167: <<< OK, it finished. -167: ............[03:04:37] Explicit valence for atom # 1 C, 5, is greater than permitted -123: processing -123: launch :0 -123: launch :1 -123: launch :2 -123: launch :3 -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) -155/208 Test #168: pyTestConformerWrap .................... Passed 0.86 sec -test 170 - Start 170: pyTestSGroups +171: [12:10:46] Warning: molecule is tagged as 3D, but all Z coords are zero +170: ............. +170: ---------------------------------------------------------------------- +170: Ran 13 tests in 0.067s +170: +170: OK +170: Testing SubstanceGroups wrapper +156/208 Test #170: pyTestSGroups .......................... Passed 1.07 sec +test 172 + Start 172: pyTestMultithreadedMolSupplier -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-x86_64-linux-gnu/Code/GraphMol/Wrap -170: Test timeout computed to be: 1500 -167: ..[03:04:37] non-ring atom 0 marked aromatic -167: [03:04:37] non-ring atom 0 marked aromatic -167: [03:04:37] -167: -167: **** -167: Range Error -167: idx -167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -167: Failed Expression: 12 < 6 -167: **** -167: -167: [03:04:37] non-ring atom 0 marked aromatic -167: [03:04:37] non-ring atom 0 marked aromatic -167: [03:04:37] -167: -167: **** -167: Range Error -167: idx -167: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -167: Failed Expression: 12 < 6 -167: **** -167: -167: ...............[03:04:37] 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: [03:04:37] 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: ..............[03:04:38] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -167: [03:04:38] Explicit valence for atom # 1 C, 5, is greater than permitted -169: .[03:04:38] +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-x86_64-linux-gnu/Code/GraphMol/Wrap +172: Test timeout computed to be: 1500 +169: .[12:10:47] 169: 169: **** 169: Range Error @@ -27556,7 +27602,7 @@ 169: Failed Expression: 0 < 0 169: **** 169: -169: .[03:04:38] +169: .[12:10:47] 169: 169: **** 169: Pre-condition Violation @@ -27565,7 +27611,7 @@ 169: Failed Expression: traj.dimension() == 3 169: **** 169: -169: ..[03:04:38] +169: ..[12:10:47] 169: 169: **** 169: Pre-condition Violation @@ -27574,7 +27620,7 @@ 169: Failed Expression: traj.dimension() == 3 169: **** 169: -169: .[03:04:38] +169: .[12:10:47] 169: 169: **** 169: Pre-condition Violation @@ -27583,7 +27629,7 @@ 169: Failed Expression: d_pos 169: **** 169: -169: [03:04:38] +169: [12:10:47] 169: 169: **** 169: Pre-condition Violation @@ -27592,7 +27638,7 @@ 169: Failed Expression: d_trajectory 169: **** 169: -169: .[03:04:38] +169: .[12:10:47] 169: 169: **** 169: Range Error @@ -27601,7 +27647,7 @@ 169: Failed Expression: 5 < 5 169: **** 169: -169: [03:04:38] +169: [12:10:47] 169: 169: **** 169: Range Error @@ -27610,7 +27656,7 @@ 169: Failed Expression: 10 < 10 169: **** 169: -169: .[03:04:38] +169: .[12:10:47] 169: 169: **** 169: Range Error @@ -27619,7 +27665,7 @@ 169: Failed Expression: 5 < 5 169: **** 169: -169: [03:04:38] +169: [12:10:47] 169: 169: **** 169: Pre-condition Violation @@ -27628,7 +27674,7 @@ 169: Failed Expression: d_trajectory->dimension() == 2 169: **** 169: -169: [03:04:38] +169: [12:10:47] 169: 169: **** 169: Pre-condition Violation @@ -27639,671 +27685,464 @@ 169: 169: . 169: ---------------------------------------------------------------------- -169: Ran 9 tests in 0.480s +169: Ran 9 tests in 0.878s 169: 169: OK 169: Testing Trajectory wrapper -156/208 Test #169: pyTestTrajectory ....................... Passed 0.86 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-x86_64-linux-gnu/Code/GraphMol/Wrap -171: Test timeout computed to be: 1500 -155: [03:04:38] ------------------------------------- -155: [03:04:38] testSegFaultInHolder -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: syntax error[03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [03:04:38] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [03:04:38] ------------------------------------- -155: [03:04:38] Results do not depend on numThreads -170: ............. -170: ---------------------------------------------------------------------- -170: Ran 13 tests in 0.050s -170: -170: OK -170: Testing SubstanceGroups wrapper -171: [03:04:38] Warning: molecule is tagged as 3D, but all Z coords are zero -157/208 Test #170: pyTestSGroups .......................... Passed 0.73 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-x86_64-linux-gnu/Code/GraphMol/Wrap -172: Test timeout computed to be: 1500 -136: Done -136: ----------------- Test Github #781: Rendering single-atom molecules -136: Done -136: ----------------- Test 3 -136: file test3_1.png gave hash 457962218U not the expected 1578780280U -136: file test3_2.png gave hash 3723407046U not the expected 1100583374U -172: .s. -172: ---------------------------------------------------------------------- -172: Ran 3 tests in 0.101s -172: -172: OK (skipped=1) -172: Testing Smiles and SD MultithreadedMolSupplier -136: file test3_3.png gave hash 715516981U not the expected 2405974883U -136: file test3_3.svg gave hash 220863844U not the expected 3967096277U -136: file test3_4.png gave hash 2817418133U not the expected 3523404550U -136: file test3_4.svg gave hash 2724848547U not the expected 1410409071U -158/208 Test #172: pyTestMultithreadedMolSupplier ......... Passed 0.54 sec +157/208 Test #169: pyTestTrajectory ....................... Passed 1.66 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-x86_64-linux-gnu/Code/GraphMol/Wrap 173: Test timeout computed to be: 1500 -158: bulk -136: file test3_5.png gave hash 818301013U not the expected 411486117U -136: file test3_6.png gave hash 2110857497U not the expected 2817453573U -136: file test3_7.png gave hash 3427920771U not the expected 285272009U -136: Done -136: ----------------- Test Github774: upside-down drawings -136: file test774_1.png gave hash 2923949014U not the expected 930347428U -136: file test774_2.png gave hash 2509515311U 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 2480095457U not the expected 4140960740U -136: file test852_2.png gave hash 3927167691U 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 2949617705U not the expected 1000110983U -136: file test860_2.png gave hash 1299641239U not the expected 4079976606U -173: [03:04:39] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [03:04:39] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [03:04:39] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -173: .[03:04:39] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [03:04:39] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [03:04:39] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -173: ..[03:04:39] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [03:04:39] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [03:04:39] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +155: [12:10:47] ------------------------------------- +155: [12:10:47] testing PatternHolder +155: [12:10:47] ------------------------------------- +155: [12:10:47] testing TautomerPatternHolder +173: [12:10:48] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [12:10:48] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [12:10:48] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: .[12:10:48] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [12:10:48] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [12:10:48] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: ..[12:10:48] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [12:10:48] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [12:10:48] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 173: . 173: ---------------------------------------------------------------------- -173: Ran 4 tests in 0.026s +173: Ran 4 tests in 0.050s 173: 173: OK -136: file test860_3.png gave hash 3063101059U 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 -159/208 Test #173: pyTestPropertyLists .................... Passed 0.52 sec +158/208 Test #173: pyTestPropertyLists .................... Passed 0.86 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-x86_64-linux-gnu/Code/GraphMol/Wrap 174: Test timeout computed to be: 1500 -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 -174: . -174: ---------------------------------------------------------------------- -174: Ran 1 test in 0.025s -174: -174: OK -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. -160/208 Test #174: pyCDXMLTest ............................ Passed 0.45 sec +172: .s. +172: ---------------------------------------------------------------------- +172: Ran 3 tests in 0.452s +172: +172: OK (skipped=1) +172: Testing Smiles and SD MultithreadedMolSupplier +155: [12:10:48] ------------------------------------- +155: [12:10:48] testSegFaultInHolder +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error[12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[12:10:48] [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: ' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: ' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: dsafsdf' +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] [12:10:48] [12:10:48] [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: SMILES Parse Error: syntax error while parsing: dsafsdf +155: SMILES Parse Error: syntax error[12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf[12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[12:10:48] SMILES Parse Error: syntax error while parsing: for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: +155: +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: dsafsdf +155: SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +159/208 Test #172: pyTestMultithreadedMolSupplier ......... Passed 1.16 sec test 175 Start 175: molStandardizeTest 175: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 175: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize 175: Test timeout computed to be: 1500 -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 73752569U not the expected 221585048U -136: file test20_2.png gave hash 2200357504U not the expected 1113799362U -136: file test20_3.png gave hash 2629540032U not the expected 1764616972U -136: file test20_4.png gave hash 70293555U not the expected 781264160U -136: Done -136: ----------------- Test 21 - different font -136: [03:04:40] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/No_Such_Font_File.ttf not found. -136: [03:04:40] 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 3308818881U not the expected 316930677U -136: file testGithub3305_2.png gave hash 2289431249U not the expected 3520446560U -136: file testGithub3305_3.png gave hash 1384561167U not the expected 3960184199U -136: file testGithub3305_4.png gave hash 818301013U not the expected 411486117U -136: file testGithub3305_5.png gave hash 1572558217U not the expected 3988290371U -136: file testGithub3305_6.png gave hash 970355724U not the expected 4125772769U -136: file testGithub3305_7.png gave hash 3830615961U 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 -161/208 Test #136: moldraw2DTest1 ......................... Passed 15.96 sec -test 176 - Start 176: molNormalizeTest - -176: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest -176: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -176: Test timeout computed to be: 1500 -176: [03:04:41] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -176: [03:04:41] Initializing Normalizer -176: [03:04:41] Running Normalizer -176: [03:04:41] Rule applied: BrokenazidetoN=N+=N- -176: [03:04:41] Initializing Normalizer -176: [03:04:41] Running Normalizer -176: [03:04:41] Initializing Normalizer -176: [03:04:41] Running Normalizer -162/208 Test #176: molNormalizeTest ....................... Passed 0.35 sec -test 177 - Start 177: molValidateTest - -177: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest -177: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -177: Test timeout computed to be: 1500 -129: ............[03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -163/208 Test #177: molValidateTest ........................ Passed 0.13 sec -test 178 - Start 178: molChargeTest - -178: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest -178: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -178: Test timeout computed to be: 1500 -164/208 Test #175: molStandardizeTest ..................... Passed 1.37 sec -test 179 - Start 179: molTautomerTest - -179: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest -179: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -179: Test timeout computed to be: 1500 -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -165/208 Test #178: molChargeTest .......................... Passed 0.21 sec -test 180 - Start 180: molStandardizeSmallTest - -180: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest -180: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -180: Test timeout computed to be: 1500 -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:41] Molecule does not have explicit Hs. Consider calling AddHs() -166/208 Test #180: molStandardizeSmallTest ................ Passed 0.11 sec -test 181 - Start 181: molFragmentTest - -181: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest -181: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -181: Test timeout computed to be: 1500 -181: [03:04:41] SMARTS Parse Error: syntax error while parsing: [Cl -181: [03:04:41] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -167/208 Test #181: molFragmentTest ........................ Passed 0.15 sec -test 182 - Start 182: molStandardizeCatchTest - -182: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest -182: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize -182: Test timeout computed to be: 1500 +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [12:10:48] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [12:10:48] ------------------------------------- +155: [12:10:48] Results do not depend on numThreads +123: processing +123: launch :0 +123: launch :1 +123: launch :2 +123: launch :3 149: VS001: PASSED 149: VS002: PASSED 149: VS003: PASSED @@ -28606,120 +28445,319 @@ 149: VS300: PASSED 149: Check finished: 0 molecules failed. 149: Failed: -168/208 Test #149: pyCIPLabelsValidation .................. Passed 12.78 sec -test 183 - Start 183: pyMolStandardize +174: . +174: ---------------------------------------------------------------------- +174: Ran 1 test in 0.035s +174: +174: OK +160/208 Test #149: pyCIPLabelsValidation .................. Passed 13.02 sec +test 176 + Start 176: molNormalizeTest -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-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -183: Test timeout computed to be: 1500 +176: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest +176: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +176: Test timeout computed to be: 1500 +176: [12:10:49] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +161/208 Test #174: pyCDXMLTest ............................ Passed 0.85 sec +test 177 + Start 177: molValidateTest + +177: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest +177: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +177: Test timeout computed to be: 1500 +158: iterative +162/208 Test #177: molValidateTest ........................ Passed 0.16 sec +test 178 + Start 178: molChargeTest + +178: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest +178: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +178: Test timeout computed to be: 1500 +176: [12:10:49] Initializing Normalizer +176: [12:10:49] Running Normalizer +176: [12:10:49] Rule applied: BrokenazidetoN=N+=N- +176: [12:10:49] Initializing Normalizer +176: [12:10:49] Running Normalizer +176: [12:10:49] Initializing Normalizer +176: [12:10:49] Running Normalizer +163/208 Test #176: molNormalizeTest ....................... Passed 0.31 sec +test 179 + Start 179: molTautomerTest + +179: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest +179: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +179: Test timeout computed to be: 1500 +164/208 Test #178: molChargeTest .......................... Passed 0.33 sec +test 180 + Start 180: molStandardizeSmallTest + +180: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest +180: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +180: Test timeout computed to be: 1500 +165/208 Test #180: molStandardizeSmallTest ................ Passed 0.14 sec +test 181 + Start 181: molFragmentTest + +181: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest +181: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +181: Test timeout computed to be: 1500 +181: [12:10:49] SMARTS Parse Error: syntax error while parsing: [Cl +181: [12:10:49] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +166/208 Test #181: molFragmentTest ........................ Passed 0.14 sec +test 182 + Start 182: molStandardizeCatchTest + +182: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest +182: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolStandardize +182: Test timeout computed to be: 1500 182: * - * - * - * m1 182: * - * - * - * m2 182: * - * - * - * m1 182: * - * - * - * m2 -158: bulk, no symmetry -182: [03:04:42] Can't kekulize mol. Unkekulized atoms: 3 7 -182: [03:04:42] Can't kekulize mol. Unkekulized atoms: 3 8 -182: [03:04:42] Can't kekulize mol. Unkekulized atoms: 2 3 4 +182: [12:10:50] Can't kekulize mol. Unkekulized atoms: 3 7 +182: [12:10:50] Can't kekulize mol. Unkekulized atoms: 3 8 +182: [12:10:50] Can't kekulize mol. Unkekulized atoms: 2 3 4 182: =============================================================================== 182: All tests passed (240 assertions in 36 test cases) 182: -169/208 Test #182: molStandardizeCatchTest ................ Passed 0.55 sec +167/208 Test #182: molStandardizeCatchTest ................ Passed 0.56 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-x86_64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +183: Test timeout computed to be: 1500 +168/208 Test #175: molStandardizeTest ..................... Passed 2.36 sec test 184 Start 184: testScaffoldNetwork 184: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 184: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork 184: Test timeout computed to be: 1500 -179: [03:04:43] Tautomer enumeration stopped at 292 tautomers: max transforms reached -158: [03:04:43] Relabelling existing label +179: [12:10:50] Tautomer enumeration stopped at 292 tautomers: max transforms reached +158: bulk +136: Done +136: ----------------- Test Github #781: Rendering single-atom molecules +183: .....[12:10:52] Tautomer enumeration stopped at 292 tautomers: max transforms reached +136: Done +136: ----------------- Test 3 +136: file test3_1.png gave hash 457962218U not the expected 1578780280U +136: file test3_2.png gave hash 3723407046U not the expected 1100583374U +136: file test3_3.png gave hash 715516981U not the expected 2405974883U +136: file test3_3.svg gave hash 220863844U not the expected 3967096277U +179: [12:10:52] Tautomer enumeration stopped at 292 tautomers: max transforms reached +136: file test3_4.png gave hash 2817418133U not the expected 3523404550U +136: file test3_4.svg gave hash 2724848547U not the expected 1410409071U +136: file test3_5.png gave hash 818301013U not the expected 411486117U +183: [12:10:52] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +136: file test3_6.png gave hash 2110857497U not the expected 2817453573U +136: file test3_7.png gave hash 3427920771U not the expected 285272009U +136: Done +136: ----------------- Test Github774: upside-down drawings +179: [12:10:52] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +136: file test774_1.png gave hash 2923949014U not the expected 930347428U +136: file test774_2.png gave hash 2509515311U 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 2480095457U not the expected 4140960740U +136: file test852_2.png gave hash 3927167691U 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 2949617705U not the expected 1000110983U +136: file test860_2.png gave hash 1299641239U not the expected 4079976606U +136: file test860_3.png gave hash 3063101059U 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 +183: .[12:10:53] Tautomer enumeration stopped at 24 tautomers: canceled +183: Enumeration was canceled due to timeout (50 ms) +136: Done +136: ----------------- Testing drawMolecules +179: [12:10:53] Tautomer enumeration stopped at 23 tautomers: canceled +179: Enumeration was canceled due to timeout (50 ms) +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. 184: =============================================================================== 184: All tests passed (266 assertions in 18 test cases) 184: -170/208 Test #184: testScaffoldNetwork .................... Passed 1.57 sec +169/208 Test #184: testScaffoldNetwork .................... Passed 2.62 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-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 185: Test timeout computed to be: 1500 -158: Best mapping -179: [03:04:44] Tautomer enumeration stopped at 292 tautomers: max transforms reached -183: .....[03:04:44] Tautomer enumeration stopped at 292 tautomers: max transforms reached -183: [03:04:44] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -185: ....... -185: ---------------------------------------------------------------------- -185: Ran 7 tests in 0.052s -185: -185: OK -179: [03:04:44] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -171/208 Test #185: pyScaffoldNetwork ...................... Passed 0.52 sec +158: bulk, no symmetry +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 73752569U not the expected 221585048U +136: file test20_2.png gave hash 2200357504U not the expected 1113799362U +136: file test20_3.png gave hash 2629540032U not the expected 1764616972U +136: file test20_4.png gave hash 70293555U not the expected 781264160U +136: Done +136: ----------------- Test 21 - different font +136: [12:10:53] Font file /build/reproducible-path/rdkit-202209.3/Data/Fonts/No_Such_Font_File.ttf not found. +136: [12:10:53] 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 3308818881U not the expected 316930677U +136: file testGithub3305_2.png gave hash 2289431249U not the expected 3520446560U +136: file testGithub3305_3.png gave hash 1384561167U not the expected 3960184199U +136: file testGithub3305_4.png gave hash 818301013U not the expected 411486117U +136: file testGithub3305_5.png gave hash 1572558217U not the expected 3988290371U +136: file testGithub3305_6.png gave hash 970355724U not the expected 4125772769U +129: ............[12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +136: file testGithub3305_7.png gave hash 3830615961U 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 +170/208 Test #136: moldraw2DTest1 ......................... Passed 22.63 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-x86_64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 186: Test timeout computed to be: 1500 -183: .[03:04:44] Tautomer enumeration stopped at 53 tautomers: canceled -183: Enumeration was canceled due to timeout (50 ms) -179: [03:04:44] Tautomer enumeration stopped at 74 tautomers: canceled -179: Enumeration was canceled due to timeout (50 ms) -186: . -186: ---------------------------------------------------------------------- -186: Ran 1 test in 0.028s -186: -186: OK -172/208 Test #186: pyScaffoldNetworkPickling .............. Passed 0.60 sec +185: ....... +185: ---------------------------------------------------------------------- +185: Ran 7 tests in 0.124s +185: +185: OK +171/208 Test #185: pyScaffoldNetwork ...................... Passed 1.01 sec test 187 Start 187: testMolEnumerator 187: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 187: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/MolEnumerator 187: Test timeout computed to be: 1500 -187: [03:04:45] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +179: 375 +179: Enumeration has completed +158: [12:10:54] Relabelling existing label +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +179: [12:10:54] Tautomer enumeration stopped at 33 tautomers: canceled +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +187: [12:10:54] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() 187: =============================================================================== 187: All tests passed (247 assertions in 12 test cases) 187: -173/208 Test #187: testMolEnumerator ...................... Passed 0.07 sec +172/208 Test #187: testMolEnumerator ...................... Passed 0.18 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-x86_64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 188: Test timeout computed to be: 1500 -155: [03:04:45] ------------------------------------- -155: [03:04:45] Results do not depend on numThreads (all same) -188: ... -188: ---------------------------------------------------------------------- -188: Ran 3 tests in 0.016s -188: -188: OK -155: [03:04:45] ------------------------------------- -155: [03:04:45] testTautomerQueries -174/208 Test #188: pyMolEnumerator ........................ Passed 0.34 sec +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +186: . +186: ---------------------------------------------------------------------- +186: Ran 1 test in 0.020s +186: +186: OK +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:10:54] Molecule does not have explicit Hs. Consider calling AddHs() +173/208 Test #186: pyScaffoldNetworkPickling .............. Passed 0.54 sec test 189 Start 189: testAbbreviations 189: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 189: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations 189: Test timeout computed to be: 1500 -155: [03:04:45] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -155: [03:04:45] ------------------------------------- -155: [03:04:45] github3881 recursive smarts with rings -189: [03:04:45] SMARTS Parse Error: syntax error while parsing: *fail -189: [03:04:45] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -175/208 Test #155: substructLibraryTest ................... Passed 15.11 sec +189: [12:10:54] SMARTS Parse Error: syntax error while parsing: *fail +189: [12:10:54] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +189: [12:10:54] no suitable SubstanceGroups found +189: =============================================================================== +189: All tests passed (195 assertions in 12 test cases) +189: +174/208 Test #189: testAbbreviations ...................... Passed 0.13 sec test 190 Start 190: pyAbbreviations 190: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 190: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 190: Test timeout computed to be: 1500 -189: [03:04:45] no suitable SubstanceGroups found -189: =============================================================================== -189: All tests passed (195 assertions in 12 test cases) -189: -176/208 Test #189: testAbbreviations ...................... Passed 0.05 sec +183: Enumeration has completed +190: ....... +190: ---------------------------------------------------------------------- +190: Ran 7 tests in 0.034s +190: +190: OK +183: [12:10:55] Tautomer enumeration stopped at 42 tautomers: canceled +188: ... +188: ---------------------------------------------------------------------- +188: Ran 3 tests in 0.048s +188: +188: OK +158: Best mapping +175/208 Test #190: pyAbbreviations ........................ Passed 0.53 sec test 191 Start 191: testQuery @@ -28743,13 +28781,20 @@ 191: XOr 191: pointer and copy foo 191: Set2 -177/208 Test #191: testQuery .............................. Passed 0.04 sec +176/208 Test #191: testQuery .............................. Passed 0.02 sec test 192 Start 192: testMatCalc 192: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc 192: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc 192: Test timeout computed to be: 1500 +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 192: 1.68022e+08 192: 1.73149e+08 192: 1.05549e+08 @@ -28795,88 +28840,58 @@ 192: 9.49496e+07 192: 2.25618e+08 192: 1.30219e+08 -178/208 Test #192: testMatCalc ............................ Passed 0.03 sec +177/208 Test #192: testMatCalc ............................ Passed 0.03 sec test 193 Start 193: pyMatCalc 193: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 193: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 193: Test timeout computed to be: 1500 -179: 375 -179: Enumeration has completed -179: [03:04:46] Tautomer enumeration stopped at 35 tautomers: canceled -190: ....... -190: ---------------------------------------------------------------------- -190: Ran 7 tests in 0.049s -190: -190: OK -179/208 Test #190: pyAbbreviations ........................ Passed 0.75 sec +178/208 Test #188: pyMolEnumerator ........................ Passed 0.95 sec test 194 Start 194: testSimDivPickers 194: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/testSimDivPickers 194: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers 194: Test timeout computed to be: 1500 -167: ...........................[03:04:46] unable to set wavy bonds for double bonds: 3 -194: [03:04:46] ------------------------------------- -194: [03:04:46] Testing github issue 1421: MaxMinPicker picking non-existent element. -167: .........[03:04:46] -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: -194: [03:04:46] Done -194: [03:04:46] ------------------------------------- -194: [03:04:46] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -194: [03:04:46] Done -180/208 Test #194: testSimDivPickers ...................... Passed 0.14 sec +194: [12:10:55] ------------------------------------- +194: [12:10:55] Testing github issue 1421: MaxMinPicker picking non-existent element. +194: [12:10:55] Done +194: [12:10:55] ------------------------------------- +194: [12:10:55] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +194: [12:10:55] Done +179/208 Test #194: testSimDivPickers ...................... Passed 0.03 sec test 195 Start 195: pickersTestsCatch 195: Test command: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 195: Working Directory: /build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/Code/SimDivPickers 195: Test timeout computed to be: 1500 -129: ...[03:04:46] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:46] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:46] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:46] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:04:46] Molecule does not have explicit Hs. Consider calling AddHs() -129: ... -129: ---------------------------------------------------------------------- -129: Ran 18 tests in 24.241s -129: -129: OK -129: Testing MolAlign Wrappers -193: ..... -193: ---------------------------------------------------------------------- -193: Ran 5 tests in 0.617s -193: -193: OK -183: Enumeration has completed -181/208 Test #193: pyMatCalc .............................. Passed 1.04 sec +180/208 Test #179: molTautomerTest ........................ Passed 6.54 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-x86_64-linux-gnu/Code/SimDivPickers/Wrap 196: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -182/208 Test #129: pyMolAlign ............................. Passed 25.03 sec +195: =============================================================================== +195: All tests passed (21267 assertions in 1 test case) +195: +181/208 Test #195: pickersTestsCatch ...................... Passed 0.33 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-x86_64-linux-gnu/Code/ML/InfoTheory/Wrap 197: Test timeout computed to be: 1500 -183: [03:04:46] Tautomer enumeration stopped at 31 tautomers: canceled -195: =============================================================================== -195: All tests passed (21267 assertions in 1 test case) -195: -183/208 Test #195: pickersTestsCatch ...................... Passed 0.28 sec +183: ...............[12:10:56] Explicit valence for atom # 1 O, 3, is greater than permitted +183: . +183: ---------------------------------------------------------------------- +183: Ran 22 tests in 5.085s +183: +183: OK +183: done +182/208 Test #183: pyMolStandardize ....................... Passed 5.70 sec test 198 Start 198: testChemicalFeatures @@ -28886,34 +28901,17 @@ 198: ----------------------------------------- 198: Test1 198: Done -184/208 Test #198: testChemicalFeatures ................... Passed 0.05 sec +183/208 Test #198: testChemicalFeatures ................... Passed 0.01 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-x86_64-linux-gnu/Code/ChemicalFeatures/Wrap 199: Test timeout computed to be: 1500 -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 -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. +196: [12:10:56] the useCache argument is deprecated and ignored 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: [03:04:47] +197: [12:10:56] 197: 197: **** 197: Invariant Violation @@ -28924,65 +28922,63 @@ 197: 197: ... 197: ---------------------------------------------------------------------- -197: Ran 5 tests in 0.068s +197: Ran 5 tests in 0.076s 197: 197: OK -25: done -25: ------------------------------------- -25: Unit test for MMFF butane scan. -199: .. -199: ---------------------------------------------------------------------- -199: Ran 2 tests in 0.001s -199: -199: OK -199: Testing ChemicalFeatures Wrapper code: -185/208 Test #197: pyRanker ............................... Passed 0.73 sec +184/208 Test #197: pyRanker ............................... Passed 0.86 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-x86_64-linux-gnu/Projects 200: Test timeout computed to be: 1500 -196: [03:04:47] the useCache argument is deprecated and ignored -186/208 Test #179: molTautomerTest ........................ Passed 6.06 sec +196: ...[12:10:56] the useCache argument is deprecated and ignored +196: [12:10:56] the useCache argument is deprecated and ignored +196: .[12:10:56] the useCache argument is deprecated and ignored +199: .. +199: ---------------------------------------------------------------------- +199: Ran 2 tests in 0.001s +199: +199: OK +199: Testing ChemicalFeatures Wrapper code: +155: [12:10:57] ------------------------------------- +155: [12:10:57] Results do not depend on numThreads (all same) +185/208 Test #199: pyFeatures ............................. Passed 0.91 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-x86_64-linux-gnu/rdkit 201: Test timeout computed to be: 1500 -187/208 Test #199: pyFeatures ............................. Passed 0.70 sec +155: [12:10:57] ------------------------------------- +155: [12:10:57] testTautomerQueries +155: [12:10:57] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +155: [12:10:57] ------------------------------------- +155: [12:10:57] github3881 recursive smarts with rings +193: ..... +193: ---------------------------------------------------------------------- +193: Ran 5 tests in 1.452s +193: +193: OK +186/208 Test #155: substructLibraryTest ................... Passed 18.27 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-x86_64-linux-gnu/rdkit 202: Test timeout computed to be: 1500 -183: ...............[03:04:47] Explicit valence for atom # 1 O, 3, is greater than permitted -183: . -183: ---------------------------------------------------------------------- -183: Ran 22 tests in 4.473s -183: -183: OK -183: done -188/208 Test #183: pyMolStandardize ....................... Passed 5.45 sec +187/208 Test #193: pyMatCalc .............................. Passed 1.96 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-x86_64-linux-gnu/rdkit 203: Test timeout computed to be: 1500 -196: ...[03:04:47] the useCache argument is deprecated and ignored -196: [03:04:47] the useCache argument is deprecated and ignored -196: .[03:04:47] the useCache argument is deprecated and ignored +25: Checking against /build/reproducible-path/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed 25: done -189/208 Test #25: testMMFFForceField ..................... Passed 37.35 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-x86_64-linux-gnu/rdkit -204: Test timeout computed to be: 1500 +25: ------------------------------------- +25: Unit tests for all MMFF constraint terms. 202: EEEEEEE 202: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -29104,51 +29100,37 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 7 tests in 0.179s +202: Ran 7 tests in 0.096s 202: 202: FAILED (errors=7) -167: ...................[03:04:48] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:48] Explicit valence for atom # 6 F, 2, is greater than permitted -167: [03:04:48] Can't kekulize mol. Unkekulized atoms: 3 4 5 -167: .[03:04:48] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [03:04:48] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [03:04:48] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [03:04:48] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [03:04:48] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [03:04:48] Warning: molecule is tagged as 3D, but all Z coords are zero +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 +203: ....... +203: ---------------------------------------------------------------------- +203: Ran 7 tests in 0.058s +203: +203: OK 201: ......................... 201: ---------------------------------------------------------------------- -201: Ran 25 tests in 0.790s +201: Ran 25 tests in 0.914s 201: 201: OK -204: .. -204: ---------------------------------------------------------------------- -204: Ran 2 tests in 0.030s -204: -204: OK -190/208 Test #201: pythonTestDirRoot ...................... Passed 1.24 sec -test 205 - Start 205: pythonTestDirSimDivFilters +188/208 Test #25: testMMFFForceField ..................... Passed 42.48 sec +test 204 + Start 204: pythonTestDirDbase -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-x86_64-linux-gnu/rdkit -205: Test timeout computed to be: 1500 -203: ....... -203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.050s -203: -203: OK -204: ........... -204: ---------------------------------------------------------------------- -204: Ran 11 tests in 0.045s -204: -204: OK -200: [03:04:49] INFO: Reading molecules and constructing molecular database. -200: -200: [03:04:49] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [03:04:49] INFO: Processing 10 molecules -200: +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-x86_64-linux-gnu/rdkit +204: Test timeout computed to be: 1500 202: EEEEEEEEEEEE 202: ====================================================================== 202: ERROR: test10_filtering (__main__.TestCase.test10_filtering) @@ -29355,73 +29337,67 @@ 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ---------------------------------------------------------------------- -202: Ran 12 tests in 0.073s +202: Ran 12 tests in 0.114s 202: 202: FAILED (errors=12) -200: [03:04:49] INFO: Generating fingerprints and descriptors: -200: -204: . -204: ---------------------------------------------------------------------- -204: Ran 1 test in 0.001s -204: -204: OK 196: ....... 196: ---------------------------------------------------------------------- -196: Ran 11 tests in 1.942s +196: Ran 11 tests in 2.336s 196: 196: OK -200: [03:04:49] INFO: Finished. -200: -191/208 Test #196: pySimDivPickers ........................ Passed 2.67 sec +189/208 Test #201: pythonTestDirRoot ...................... Passed 1.64 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-x86_64-linux-gnu/rdkit +205: Test timeout computed to be: 1500 +190/208 Test #196: pySimDivPickers ........................ Passed 2.92 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-x86_64-linux-gnu/rdkit 206: Test timeout computed to be: 1500 +200: [12:10:59] INFO: Reading molecules and constructing molecular database. +200: +200: [12:10:59] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [12:10:59] INFO: Processing 10 molecules +200: +204: .. +204: ---------------------------------------------------------------------- +204: Ran 2 tests in 0.028s +204: +204: 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 0.005s +203: Ran 34 tests in 0.019s 203: 203: 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 0.027s -204: -204: OK 206: ............. 206: ---------------------------------------------------------------------- -206: Ran 13 tests in 0.011s +206: Ran 13 tests in 0.017s 206: 206: OK -204: ...... -204: ---------------------------------------------------------------------- -204: Ran 6 tests in 0.007s -204: -204: OK -192/208 Test #204: pythonTestDirDbase ..................... Passed 1.57 sec +200: [12:10:59] INFO: Generating fingerprints and descriptors: +200: +191/208 Test #205: pythonTestDirSimDivFilters ............. Passed 0.69 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-x86_64-linux-gnu/rdkit 207: Test timeout computed to be: 1500 -193/208 Test #205: pythonTestDirSimDivFilters ............. Passed 1.11 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-x86_64-linux-gnu/rdkit/Chem -208: Test timeout computed to be: 1500 -203: ..... -203: ---------------------------------------------------------------------- -203: Ran 5 tests in 0.019s -203: -203: OK +204: ........... +204: ---------------------------------------------------------------------- +204: Ran 11 tests in 0.024s +204: +204: OK +200: [12:10:59] INFO: Finished. +200: 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)) @@ -29448,72 +29424,129 @@ 202: Ran 1 test in 0.103s 202: 202: FAILED (failures=1) -157: ......[03:04:50] -157: -157: **** -157: Pre-condition Violation -157: RingInfo not initialized -157: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -157: Failed Expression: df_init -157: **** -157: -157: [03:04:50] -157: -157: **** -157: Pre-condition Violation -157: RingInfo not initialized -157: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -157: Failed Expression: df_init -157: **** -157: -203: ....... +204: . +204: ---------------------------------------------------------------------- +204: Ran 1 test in 0.002s +204: +204: OK +203: ..... 203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.001s +203: Ran 5 tests in 0.008s 203: 203: OK -208: ....... -208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.099s -208: -208: 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 0.043s +204: +204: OK 206: ........... 206: ---------------------------------------------------------------------- -206: Ran 11 tests in 0.067s +206: Ran 11 tests in 0.127s 206: 206: OK -194/208 Test #203: pythonTestDirDataStructs ............... Passed 2.75 sec -195/208 Test #206: pythonTestDirVLib ...................... Passed 1.23 sec -196/208 Test #158: testRGroupDecomp ....................... Passed 19.82 sec -207: .. -207: ---------------------------------------------------------------------- -207: Ran 2 tests in 0.228s -207: -207: OK +204: ...... +204: ---------------------------------------------------------------------- +204: Ran 6 tests in 0.010s +204: +204: OK +203: ....... +203: ---------------------------------------------------------------------- +203: Ran 7 tests in 0.002s +203: +203: OK 202: ... 202: ---------------------------------------------------------------------- 202: Ran 3 tests in 0.002s 202: 202: OK -208: ...... -208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.082s -208: -208: OK -197/208 Test #207: pythonTestSping ........................ Passed 1.33 sec -200: [03:04:51] INFO: Reading molecules and constructing molecular database. +192/208 Test #204: pythonTestDirDbase ..................... Passed 1.76 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-x86_64-linux-gnu/rdkit/Chem +208: Test timeout computed to be: 1500 +193/208 Test #203: pythonTestDirDataStructs ............... Passed 2.94 sec +194/208 Test #206: pythonTestDirVLib ...................... Passed 1.69 sec +200: [12:11:01] INFO: Reading molecules and constructing molecular database. 200: -200: [03:04:51] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [12:11:01] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [03:04:51] INFO: Processing 163 molecules +200: [12:11:01] INFO: Processing 163 molecules 200: 202: ........ 202: ---------------------------------------------------------------------- 202: Ran 8 tests in 0.001s 202: 202: OK -200: [03:04:51] INFO: done 100 +200: [12:11:01] INFO: done 100 +200: +207: .. +207: ---------------------------------------------------------------------- +207: Ran 2 tests in 0.541s +207: +207: OK +200: [12:11:01] INFO: Generating fingerprints and descriptors: 200: -208: ....[03:04:51] +129: ...[12:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +195/208 Test #207: pythonTestSping ........................ Passed 2.09 sec +208: ....... +208: ---------------------------------------------------------------------- +208: Ran 7 tests in 0.238s +208: +208: OK +129: ... +129: ---------------------------------------------------------------------- +129: Ran 18 tests in 31.192s +129: +129: OK +129: Testing MolAlign Wrappers +196/208 Test #129: pyMolAlign ............................. Passed 32.16 sec +167: ...........................[12:11:02] unable to set wavy bonds for double bonds: 3 +167: .........[12:11:02] +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: +202: .... +202: ---------------------------------------------------------------------- +202: Ran 4 tests in 0.840s +202: +202: OK +208: ...... +208: ---------------------------------------------------------------------- +208: Ran 6 tests in 0.110s +208: +208: OK +157: ......[12:11:02] +157: +157: **** +157: Pre-condition Violation +157: RingInfo not initialized +157: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +157: Failed Expression: df_init +157: **** +157: +157: [12:11:02] +157: +157: **** +157: Pre-condition Violation +157: RingInfo not initialized +157: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +157: Failed Expression: df_init +157: **** +157: +208: ....[12:11:03] 208: 208: **** 208: Pre-condition Violation @@ -29524,32 +29557,9 @@ 208: 208: . 208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.010s -208: -208: OK -200: [03:04:51] INFO: Generating fingerprints and descriptors: -200: -208: .... -208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.010s -208: -208: OK -208: .. -208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.014s +208: Ran 5 tests in 0.031s 208: 208: OK -202: .... -202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.629s -202: -202: OK -208: ...................... -208: ---------------------------------------------------------------------- -208: Ran 22 tests in 0.039s -208: -208: OK -198/208 Test #171: pyTestThreads .......................... Passed 14.41 sec 202: E.EEE 202: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -29608,34 +29618,23 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.004s +202: Ran 5 tests in 0.005s 202: 202: FAILED (errors=4) -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-x86_64-linux-gnu/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-x86_64-linux-gnu/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: +167: ...................[12:11:04] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:04] Explicit valence for atom # 6 F, 2, is greater than permitted +167: [12:11:04] Can't kekulize mol. Unkekulized atoms: 3 4 5 +167: .[12:11:04] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [12:11:04] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [12:11:04] Warning: molecule is tagged as 3D, but all Z coords are zero +208: .... 208: ---------------------------------------------------------------------- -208: Ran 25 tests in 0.155s +208: Ran 4 tests in 0.034s 208: -208: FAILED (errors=1, skipped=3) +208: OK +167: [12:11:04] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [12:11:04] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [12:11:04] Warning: molecule is tagged as 3D, but all Z coords are zero 202: .......E. 202: ====================================================================== 202: ERROR: test_RandomizeActivities (__main__.TestCase.test_RandomizeActivities) @@ -29648,24 +29647,56 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 9 tests in 0.006s +202: Ran 9 tests in 0.014s 202: 202: FAILED (errors=1) +208: .. +208: ---------------------------------------------------------------------- +208: Ran 2 tests in 0.026s +208: +208: OK 202: ............ 202: ---------------------------------------------------------------------- -202: Ran 12 tests in 0.004s +202: Ran 12 tests in 0.008s 202: 202: OK -208: ..s +208: ...................... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.199s +208: Ran 22 tests in 0.042s 208: -208: OK (skipped=1) +208: OK +197/208 Test #171: pyTestThreads .......................... Passed 19.01 sec 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.036s +202: Ran 5 tests in 0.114s 202: 202: OK +198/208 Test #158: testRGroupDecomp ....................... Passed 25.59 sec +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-x86_64-linux-gnu/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-x86_64-linux-gnu/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 0.336s +208: +208: FAILED (errors=1, skipped=3) 202: ********************************************************************** 202: File "/build/reproducible-path/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 208, in __main__.SplitDbData 202: Failed example: @@ -29862,11 +29893,11 @@ 202: !!! TEST FAILURE: python UnitTestFilter.py {} 202: !!! TEST FAILURE: python UnitTestMLData.py {} 202: !!! TEST FAILURE: python SplitData.py {} -208: ................................... +208: ..s 208: ---------------------------------------------------------------------- -208: Ran 35 tests in 1.062s +208: Ran 3 tests in 0.411s 208: -208: OK +208: OK (skipped=1) 202: . 202: ---------------------------------------------------------------------- 202: Ran 1 test in 0.000s @@ -29874,194 +29905,41 @@ 202: OK 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.002s +202: Ran 6 tests in 0.006s 202: 202: OK -200: [03:04:55] INFO: Finished. +200: [12:11:07] INFO: Finished. 200: -208: .... -208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.042s -208: -208: OK -208: . -208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.017s -208: -208: OK -208: ....... -208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.076s -208: -208: OK 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 1.233s +202: Ran 4 tests in 1.046s 202: 202: OK -208: ... +208: ................................... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.061s +208: Ran 35 tests in 1.101s 208: 208: OK -167: ...............[03:04:57] -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: [03:04:57] -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: [03:04:57] -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: [03:04:57] -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: [03:04:57] -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: .....[03:04:57] -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: ......[03:04:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -167: [03:04:57] ERROR: Smiles parse error on line 0 -167: [03:04:57] ERROR: Cannot create molecule from : 'c1ccccc' -167: [03:04:57] SMILES Parse Error: extra open parentheses for input: 'C(C' -167: [03:04:57] ERROR: Smiles parse error on line 3 -167: [03:04:57] ERROR: Cannot create molecule from : 'C(C' -167: [03:04:57] Explicit valence for atom # 1 C, 5, is greater than permitted -167: [03:04:57] ERROR: Could not sanitize molecule on line 6 -167: [03:04:57] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -167: [03:04:57] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -167: [03:04:57] ERROR: Smiles parse error on line 0 -167: [03:04:57] ERROR: Cannot create molecule from : 'c1ccccc' -167: [03:04:57] SMILES Parse Error: extra open parentheses for input: 'C(C' -167: [03:04:57] ERROR: Smiles parse error on line 3 -167: [03:04:57] ERROR: Cannot create molecule from : 'C(C' -167: [03:04:57] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -167: [03:04:57] ERROR: Smiles parse error on line 6 -167: [03:04:57] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -167: [03:04:57] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:57] ERROR: Could not sanitize molecule ending on line 21 -167: [03:04:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:57] ERROR: EOF hit while reading atoms -167: [03:04:57] ERROR: moving to the beginning of the next molecule -167: [03:04:57] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:57] ERROR: Could not sanitize molecule ending on line 21 -167: [03:04:57] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:57] ERROR: EOF hit while reading atoms -167: [03:04:57] ERROR: moving to the beginning of the next molecule -167: ....[03:04:57] -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: -167: ......[03:04:57] -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: ..[03:04:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.054s +202: Ran 6 tests in 0.055s 202: 202: OK -167: .................[03:04:57] SMILES Parse Error: unclosed ring for input: 'C1CC' -167: ......[03:04:57] WARNING: not removing hydrogen atom without neighbors -167: [03:04:57] WARNING: not removing hydrogen atom with dummy atom neighbors -167: [03:04:57] WARNING: not removing hydrogen atom with wedged bond -167: [03:04:57] WARNING: not removing hydrogen atom without neighbors -167: [03:04:57] WARNING: not removing hydrogen atom with dummy atom neighbors -167: .....[03:04:58] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: .[03:04:58] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:58] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:58] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:58] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [03:04:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: [03:04:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: [03:04:58] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: ..........[03:04:58] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -167: [03:04:58] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -167: .[03:04:58] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -167: [03:04:58] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -167: ..[03:04:58] SMILES Parse Error: syntax error while parsing: error -167: [03:04:58] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -167: [03:04:58] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -167: [03:04:58] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -167: [03:04:58] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -167: ...........[03:04:58] SMILES Parse Error: syntax error while parsing: garbage_0 -167: [03:04:58] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -167: [03:04:58] SMILES Parse Error: syntax error while parsing: garbage_2 -167: [03:04:58] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -167: [03:04:58] SMILES Parse Error: syntax error while parsing: garbage_4 -167: [03:04:58] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -167: ......... -167: ---------------------------------------------------------------------- -167: Ran 228 tests in 20.606s -167: -167: OK -167: 406 -167: supplier: -167: supplier: -167: supplier: -199/208 Test #167: pyGraphMolWrap ......................... Passed 21.81 sec -208: .ss.ss....... +208: .... 208: ---------------------------------------------------------------------- -208: Ran 13 tests in 1.192s +208: Ran 4 tests in 0.026s 208: -208: OK (skipped=4) +208: OK +208: . +208: ---------------------------------------------------------------------- +208: Ran 1 test in 0.026s +208: +208: OK 202: .. 202: ---------------------------------------------------------------------- -202: Ran 2 tests in 0.393s +202: Ran 2 tests in 0.368s 202: 202: OK -208: [03:04:59] Molecule does not have explicit Hs. Consider calling AddHs() -208: .[03:04:59] Molecule does not have explicit Hs. Consider calling AddHs() 202: ........E. 202: ====================================================================== 202: ERROR: test8RandomForest (__main__.TestCase.test8RandomForest) @@ -30078,20 +29956,30 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 10 tests in 0.027s +202: Ran 10 tests in 0.016s 202: 202: FAILED (errors=1) +208: ....... +208: ---------------------------------------------------------------------- +208: Ran 7 tests in 0.115s +208: +208: OK 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.086s +202: Ran 5 tests in 0.095s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestQuantTree.py {} 202: .. 202: ---------------------------------------------------------------------- -202: Ran 2 tests in 0.008s +202: Ran 2 tests in 0.009s 202: 202: OK +208: ... +208: ---------------------------------------------------------------------- +208: Ran 3 tests in 0.118s +208: +208: OK 202: ....Traceback (most recent call last): 202: File "/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/rdkit/ML/Descriptors/MoleculeDescriptors.py", line 88, in CalcDescriptors 202: res[i] = fn(mol) @@ -30118,19 +30006,12 @@ 202: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 202: 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.016s +202: Ran 5 tests in 0.040s 202: 202: FAILED (errors=1) -127: --------------------------------- -127: test O3A multithreading bug -127: -127: --------------------------------- -127: testCrippenO3A multithreading -127: -127: generating reference data 202: ... 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.011s +202: Ran 3 tests in 0.029s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestMolDescriptors.py {} @@ -30166,14 +30047,157 @@ 202: !!! TEST FAILURE: python UnitTestCorrMatGen.py {} 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.468s +202: Ran 6 tests in 0.620s 202: 202: OK -127: processing -127: launch :0 -127: launch :1 -127: launch :2 -127: launch :3 +208: .ss.ss....... +208: ---------------------------------------------------------------------- +208: Ran 13 tests in 2.731s +208: +208: OK (skipped=4) +167: ...............[12:11:16] +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: [12:11:16] +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: [12:11:16] +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: [12:11:16] +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: [12:11:16] +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: .....[12:11:16] +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: ......[12:11:16] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +167: [12:11:16] ERROR: Smiles parse error on line 0 +167: [12:11:16] ERROR: Cannot create molecule from : 'c1ccccc' +167: [12:11:16] SMILES Parse Error: extra open parentheses for input: 'C(C' +167: [12:11:16] ERROR: Smiles parse error on line 3 +167: [12:11:16] ERROR: Cannot create molecule from : 'C(C' +167: [12:11:16] Explicit valence for atom # 1 C, 5, is greater than permitted +167: [12:11:16] ERROR: Could not sanitize molecule on line 6 +167: [12:11:16] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +167: [12:11:16] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +167: [12:11:16] ERROR: Smiles parse error on line 0 +167: [12:11:16] ERROR: Cannot create molecule from : 'c1ccccc' +167: [12:11:16] SMILES Parse Error: extra open parentheses for input: 'C(C' +167: [12:11:16] ERROR: Smiles parse error on line 3 +167: [12:11:16] ERROR: Cannot create molecule from : 'C(C' +167: [12:11:16] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +167: [12:11:16] ERROR: Smiles parse error on line 6 +167: [12:11:16] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +167: [12:11:16] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] ERROR: Could not sanitize molecule ending on line 21 +167: [12:11:16] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] ERROR: EOF hit while reading atoms +167: [12:11:16] ERROR: moving to the beginning of the next molecule +167: [12:11:16] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] ERROR: Could not sanitize molecule ending on line 21 +167: [12:11:16] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] ERROR: EOF hit while reading atoms +167: [12:11:16] ERROR: moving to the beginning of the next molecule +167: ....[12:11:16] +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: +167: ......[12:11:16] +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: ..[12:11:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +167: .................[12:11:16] SMILES Parse Error: unclosed ring for input: 'C1CC' +167: ......[12:11:16] WARNING: not removing hydrogen atom without neighbors +167: [12:11:16] WARNING: not removing hydrogen atom with dummy atom neighbors +167: [12:11:16] WARNING: not removing hydrogen atom with wedged bond +167: [12:11:16] WARNING: not removing hydrogen atom without neighbors +167: [12:11:16] WARNING: not removing hydrogen atom with dummy atom neighbors +208: [12:11:16] Molecule does not have explicit Hs. Consider calling AddHs() +208: .[12:11:16] Molecule does not have explicit Hs. Consider calling AddHs() +167: .....[12:11:16] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: .[12:11:16] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [12:11:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: [12:11:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: [12:11:16] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: ..........[12:11:16] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +167: [12:11:16] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +167: .[12:11:16] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +167: [12:11:16] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +167: ..[12:11:16] SMILES Parse Error: syntax error while parsing: error +167: [12:11:16] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +167: [12:11:16] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +167: [12:11:16] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +167: [12:11:16] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +167: ...........[12:11:16] SMILES Parse Error: syntax error while parsing: garbage_0 +167: [12:11:16] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +167: [12:11:16] SMILES Parse Error: syntax error while parsing: garbage_2 +167: [12:11:16] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +167: [12:11:16] SMILES Parse Error: syntax error while parsing: garbage_4 +167: [12:11:16] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +167: ......... +167: ---------------------------------------------------------------------- +167: Ran 228 tests in 31.795s +167: +167: OK +167: 1 +167: supplier: +167: supplier: +167: supplier: +199/208 Test #167: pyGraphMolWrap ......................... Passed 33.37 sec 202: ...EE.. 202: ====================================================================== 202: ERROR: testPerm1 (__main__.TestCase.testPerm1) @@ -30192,13 +30216,25 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 7 tests in 0.101s +202: Ran 7 tests in 0.259s 202: 202: FAILED (errors=2) 202: !!! TEST FAILURE: python UnitTestPackage.py {} +202: .... +202: ---------------------------------------------------------------------- +202: Ran 4 tests in 0.014s +202: +202: OK +127: --------------------------------- +127: test O3A multithreading bug +127: +127: --------------------------------- +127: testCrippenO3A multithreading +127: +127: generating reference data 157: ............ 157: ---------------------------------------------------------------------- -157: Ran 18 tests in 31.970s +157: Ran 18 tests in 41.577s 157: 157: OK 157: Testing atom rings @@ -30206,74 +30242,17 @@ 157: searching atom rings 157: searching bond rings 157: done -200/208 Test #157: pySubstructLibrary ..................... Passed 32.69 sec -202: .... -202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.014s -202: -202: OK -125: .......[03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: [03:05:04] Molecule does not have explicit Hs. Consider calling AddHs() -125: . -125: ---------------------------------------------------------------------- -125: Ran 18 tests in 42.876s -125: -125: OK -201/208 Test #125: pyDistGeomHelpers ...................... Passed 43.65 sec -200: .........[03:05:06] INFO: Reading molecules and constructing molecular database. -200: -200: [03:05:06] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [03:05:06] INFO: Processing 10 molecules -200: -200: [03:05:06] INFO: Generating fingerprints and descriptors: -200: -200: [03:05:06] INFO: Finished. -200: -200: [03:05:07] INFO: Reading molecules and constructing molecular database. -200: -200: [03:05:07] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [03:05:07] INFO: Processing 10 molecules -200: -200: [03:05:07] INFO: Generating fingerprints and descriptors: -200: -200: [03:05:07] INFO: Finished. -200: +200/208 Test #157: pySubstructLibrary ..................... Passed 42.17 sec +127: processing +127: launch :0 +127: launch :1 +127: launch :2 +127: launch :3 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 4.083s +202: Ran 5 tests in 4.387s 202: 202: OK -200: [03:05:08] INFO: Reading molecules and constructing molecular database. -200: -200: [03:05:08] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [03:05:08] INFO: Processing 10 molecules -200: -200: [03:05:08] INFO: Generating fingerprints and descriptors: -200: -200: [03:05:08] INFO: Finished. -200: 202: .... 202: ---------------------------------------------------------------------- 202: Ran 4 tests in 0.002s @@ -30286,7 +30265,7 @@ 202: OK 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.007s +202: Ran 4 tests in 0.005s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestBuildComposite.py {} @@ -30297,7 +30276,7 @@ 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'} -202/208 Test #202: pythonTestDirML ........................***Failed 21.78 sec +201/208 Test #202: pythonTestDirML ........................***Failed 26.66 sec EEEEEEE ====================================================================== ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -30419,7 +30398,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 7 tests in 0.179s +Ran 7 tests in 0.096s FAILED (errors=7) EEEEEEEEEEEE @@ -30628,7 +30607,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 12 tests in 0.073s +Ran 12 tests in 0.114s FAILED (errors=12) Traceback (most recent call last): @@ -30669,7 +30648,7 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.629s +Ran 4 tests in 0.840s OK E.EEE @@ -30730,7 +30709,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 5 tests in 0.004s +Ran 5 tests in 0.005s FAILED (errors=4) .......E. @@ -30745,17 +30724,17 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 9 tests in 0.006s +Ran 9 tests in 0.014s FAILED (errors=1) ............ ---------------------------------------------------------------------- -Ran 12 tests in 0.004s +Ran 12 tests in 0.008s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.036s +Ran 5 tests in 0.114s OK ********************************************************************** @@ -30961,22 +30940,22 @@ OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.002s +Ran 6 tests in 0.006s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 1.233s +Ran 4 tests in 1.046s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.054s +Ran 6 tests in 0.055s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.393s +Ran 2 tests in 0.368s OK ........E. @@ -30995,18 +30974,18 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 10 tests in 0.027s +Ran 10 tests in 0.016s FAILED (errors=1) ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.086s +Ran 5 tests in 0.095s OK !!! TEST FAILURE: python UnitTestQuantTree.py {} .. ---------------------------------------------------------------------- -Ran 2 tests in 0.008s +Ran 2 tests in 0.009s OK ....Traceback (most recent call last): @@ -31035,12 +31014,12 @@ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- -Ran 5 tests in 0.016s +Ran 5 tests in 0.040s FAILED (errors=1) ... ---------------------------------------------------------------------- -Ran 3 tests in 0.011s +Ran 3 tests in 0.029s OK !!! TEST FAILURE: python UnitTestMolDescriptors.py {} @@ -31076,7 +31055,7 @@ !!! TEST FAILURE: python UnitTestCorrMatGen.py {} ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.468s +Ran 6 tests in 0.620s OK ...EE.. @@ -31097,7 +31076,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 7 tests in 0.101s +Ran 7 tests in 0.259s FAILED (errors=2) !!! TEST FAILURE: python UnitTestPackage.py {} @@ -31108,7 +31087,7 @@ OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 4.083s +Ran 5 tests in 4.387s OK .... @@ -31123,7 +31102,7 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.007s +Ran 4 tests in 0.005s OK !!! TEST FAILURE: python UnitTestBuildComposite.py {} @@ -31135,86 +31114,143 @@ !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'} !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -200: [03:05:09] INFO: Reading molecules and constructing molecular database. +200: .........[12:11:24] INFO: Reading molecules and constructing molecular database. +200: +200: [12:11:24] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [12:11:24] INFO: Processing 10 molecules +200: +200: [12:11:24] INFO: Generating fingerprints and descriptors: +200: +200: [12:11:24] INFO: Finished. +200: +200: [12:11:26] INFO: Reading molecules and constructing molecular database. +200: +200: [12:11:26] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [12:11:26] INFO: Processing 10 molecules 200: -200: [03:05:09] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [12:11:26] INFO: Generating fingerprints and descriptors: 200: -200: [03:05:09] INFO: Generating fingerprints and descriptors: +200: [12:11:26] INFO: Finished. 200: -200: [03:05:09] INFO: Finished. +200: [12:11:28] INFO: Reading molecules and constructing molecular database. 200: -200: [03:05:10] INFO: Reading molecules and constructing molecular database. +200: [12:11:28] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [03:05:10] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [12:11:28] INFO: Processing 10 molecules 200: -200: [03:05:10] INFO: Generating fingerprints and descriptors: +200: [12:11:28] INFO: Generating fingerprints and descriptors: 200: -200: [03:05:10] INFO: Finished. +200: [12:11:28] INFO: Finished. 200: -200: .[03:05:11] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. +125: .......[12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: [12:11:28] Molecule does not have explicit Hs. Consider calling AddHs() +125: . +125: ---------------------------------------------------------------------- +125: Ran 18 tests in 59.626s +125: +125: OK +202/208 Test #125: pyDistGeomHelpers ...................... Passed 60.73 sec +200: [12:11:29] INFO: Reading molecules and constructing molecular database. +200: +200: [12:11:29] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [12:11:29] INFO: Generating fingerprints and descriptors: +200: +200: [12:11:29] INFO: Finished. +200: +200: [12:11:30] INFO: Reading molecules and constructing molecular database. 200: -200: [03:05:11] INFO: Reading molecules and constructing molecular database. +200: [12:11:30] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [03:05:11] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [12:11:30] INFO: Generating fingerprints and descriptors: 200: -200: [03:05:11] INFO: Processing 163 molecules +200: [12:11:30] INFO: Finished. 200: -200: [03:05:12] INFO: done 100 +200: .[12:11:31] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 200: -200: [03:05:12] INFO: Generating fingerprints and descriptors: +200: [12:11:31] INFO: Reading molecules and constructing molecular database. 200: -200: [03:05:12] INFO: Finished. +200: [12:11:31] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: .[03:05:14] INFO: Reading molecules and constructing molecular database. +200: [12:11:31] INFO: Processing 163 molecules 200: -200: [03:05:14] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [12:11:31] INFO: done 100 200: -200: [03:05:14] INFO: Processing 10 molecules +200: [12:11:32] INFO: Generating fingerprints and descriptors: 200: -200: [03:05:14] INFO: Generating fingerprints and descriptors: +200: [12:11:32] INFO: Finished. 200: -200: [03:05:14] INFO: Finished. +200: .[12:11:35] INFO: Reading molecules and constructing molecular database. 200: -200: [03:05:15] INFO: Reading molecules and constructing molecular database. +200: [12:11:35] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [03:05:15] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [12:11:35] INFO: Processing 10 molecules 200: -200: [03:05:15] INFO: Processing 10 molecules +200: [12:11:35] INFO: Generating fingerprints and descriptors: 200: -200: [03:05:15] INFO: Generating fingerprints and descriptors: +200: [12:11:35] INFO: Finished. 200: -200: [03:05:15] INFO: Finished. +200: [12:11:37] INFO: Reading molecules and constructing molecular database. +200: +200: [12:11:37] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [12:11:37] INFO: Processing 10 molecules +200: +200: [12:11:37] INFO: Generating fingerprints and descriptors: +200: +200: [12:11:37] INFO: Finished. 200: 200: . 200: ---------------------------------------------------------------------- -200: Ran 12 tests in 27.499s +200: Ran 12 tests in 40.632s 200: 200: OK -203/208 Test #200: pythonTestDbCLI ........................ Passed 28.10 sec +203/208 Test #200: pythonTestDbCLI ........................ Passed 41.17 sec 127: --------------------------------- 127: test getO3AForProbeConfs 127: 127: *********************************************************** -204/208 Test #127: testO3AAlign ........................... Passed 57.47 sec -29: [03:05:34] Finished -29: [03:05:34] ------------------------------------- -29: [03:05:34] Test github1843: RWMol.clear() should not destroy ring pointer. -29: [03:05:34] Finished -205/208 Test #29: graphmolTest1 .......................... Passed 83.38 sec -208: ..................[03:05:51] WARNING: More than one matching pattern found - picking one +204/208 Test #127: testO3AAlign ........................... Passed 74.12 sec +29: [12:12:14] Finished +29: [12:12:14] ------------------------------------- +29: [12:12:14] Test github1843: RWMol.clear() should not destroy ring pointer. +29: [12:12:14] Finished +205/208 Test #29: graphmolTest1 .......................... Passed 117.86 sec +208: ..................[12:12:21] WARNING: More than one matching pattern found - picking one 208: -208: [03:05:51] WARNING: More than one matching pattern found - picking one +208: [12:12:21] WARNING: More than one matching pattern found - picking one 208: -208: .[03:05:51] WARNING: More than one matching pattern found - picking one +208: .[12:12:21] WARNING: More than one matching pattern found - picking one 208: 208: ... 208: ---------------------------------------------------------------------- -208: Ran 23 tests in 57.684s +208: Ran 23 tests in 71.041s 208: 208: OK -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) @@ -31234,7 +31270,7 @@ 208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 208: 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.122s +208: Ran 8 tests in 0.158s 208: 208: FAILED (errors=1) 208: Traceback (most recent call last): @@ -31269,10 +31305,10 @@ 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..[03:06:02] WARNING: not removing hydrogen atom without neighbors -208: [03:06:02] WARNING: not removing hydrogen atom without neighbors -208: [03:06:02] WARNING: not removing hydrogen atom without neighbors -208: ....[03:06:02] WARNING: not removing hydrogen atom without neighbors +208: F..[12:12:33] WARNING: not removing hydrogen atom without neighbors +208: [12:12:33] WARNING: not removing hydrogen atom without neighbors +208: [12:12:33] WARNING: not removing hydrogen atom without neighbors +208: ....[12:12:33] WARNING: not removing hydrogen atom without neighbors 208: ...... 208: ====================================================================== 208: FAIL: testBadAtomHandling (__main__.TestCase.testBadAtomHandling) @@ -31329,17 +31365,17 @@ 208: AssertionError: SMILES: CCC; Descriptor: Ipc 208: 208: ---------------------------------------------------------------------- -208: Ran 14 tests in 4.585s +208: Ran 14 tests in 4.964s 208: 208: FAILED (failures=2) 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 2.455s +208: Ran 4 tests in 1.775s 208: 208: OK 208: ...... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.368s +208: Ran 6 tests in 0.393s 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. @@ -31348,30 +31384,24 @@ 208: antibiotics = antibiotics.append({ 208: :1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. 208: antibiotics = antibiotics.append({ -123: [03:06:11] done 208: .......s..s........ 208: ---------------------------------------------------------------------- -208: Ran 26 tests in 3.095s +208: Ran 26 tests in 4.328s 208: 208: OK (skipped=2) +123: [12:12:47] done 123: CNC[C@H]1CC[C@H](C[NH3+])CC1 123: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 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 -123: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 -123: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O -123: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O -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 -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 -208: .............F[03:06:27] WARNING: More than one matching pattern found - picking one +208: .............F[12:13:04] WARNING: More than one matching pattern found - picking one 208: -208: [03:06:27] WARNING: More than one matching pattern found - picking one +208: [12:13:04] WARNING: More than one matching pattern found - picking one 208: -208: ..[03:06:27] Molecule does not have explicit Hs. Consider calling AddHs() -208: [03:06:27] Molecule does not have explicit Hs. Consider calling AddHs() -208: [03:06:27] Molecule does not have explicit Hs. Consider calling AddHs() -208: [03:06:27] Molecule does not have explicit Hs. Consider calling AddHs() +208: ..[12:13:04] Molecule does not have explicit Hs. Consider calling AddHs() +208: [12:13:04] Molecule does not have explicit Hs. Consider calling AddHs() +208: [12:13:04] Molecule does not have explicit Hs. Consider calling AddHs() +208: [12:13:04] Molecule does not have explicit Hs. Consider calling AddHs() 208: ......... 208: ====================================================================== 208: FAIL: FindBRICSBonds (rdkit.Chem.BRICS) @@ -31400,282 +31430,286 @@ 208: 208: 208: ---------------------------------------------------------------------- -208: Ran 25 tests in 15.528s +208: Ran 25 tests in 19.665s 208: 208: FAILED (failures=1) +123: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.067s +208: Ran 2 tests in 0.070s 208: 208: OK +123: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O 208: ..s... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.960s +208: Ran 6 tests in 1.374s 208: 208: OK (skipped=1) -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: ..[03:06:29] WARNING: not removing hydrogen atom without neighbors -208: .[03:06:29] WARNING: not removing hydrogen atom without neighbors -208: .[03:06:29] WARNING: no name column found on line 1 -208: [03:06:29] WARNING: no name column found on line 2 -208: [03:06:29] WARNING: no name column found on line 3 -208: [03:06:29] WARNING: no name column found on line 4 -208: [03:06:29] WARNING: no name column found on line 5 -208: [03:06:29] WARNING: no name column found on line 6 -208: [03:06:29] WARNING: no name column found on line 7 -208: [03:06:29] WARNING: no name column found on line 8 -208: [03:06:29] WARNING: no name column found on line 9 -208: [03:06:29] WARNING: no name column found on line 10 -208: [03:06:29] WARNING: no name column found on line 11 -208: [03:06:29] WARNING: no name column found on line 12 -208: [03:06:29] WARNING: no name column found on line 13 -208: [03:06:29] WARNING: no name column found on line 14 -208: [03:06:29] WARNING: no name column found on line 15 -208: [03:06:29] WARNING: no name column found on line 16 -208: [03:06:29] WARNING: no name column found on line 17 -208: [03:06:29] WARNING: no name column found on line 18 -208: [03:06:29] WARNING: no name column found on line 19 -208: [03:06:29] WARNING: no name column found on line 20 -208: [03:06:29] WARNING: no name column found on line 21 -208: [03:06:29] WARNING: no name column found on line 22 -208: [03:06:29] WARNING: no name column found on line 23 -208: [03:06:29] WARNING: no name column found on line 24 -208: [03:06:29] WARNING: no name column found on line 25 -208: [03:06:29] WARNING: no name column found on line 26 -208: [03:06:29] WARNING: no name column found on line 27 -208: [03:06:29] WARNING: no name column found on line 28 -208: [03:06:29] WARNING: no name column found on line 29 -208: [03:06:29] WARNING: no name column found on line 30 -208: [03:06:29] WARNING: no name column found on line 31 -208: [03:06:29] WARNING: no name column found on line 32 -208: [03:06:29] WARNING: no name column found on line 33 -208: [03:06:29] WARNING: no name column found on line 34 -208: [03:06:29] WARNING: no name column found on line 35 -208: [03:06:29] WARNING: no name column found on line 36 -208: [03:06:29] WARNING: no name column found on line 37 -208: [03:06:29] WARNING: no name column found on line 38 -208: [03:06:29] WARNING: no name column found on line 39 -208: [03:06:29] WARNING: no name column found on line 40 -208: [03:06:29] WARNING: no name column found on line 41 -208: [03:06:29] WARNING: no name column found on line 42 -208: [03:06:29] WARNING: no name column found on line 43 -208: [03:06:29] WARNING: no name column found on line 44 -208: [03:06:29] WARNING: no name column found on line 45 -208: [03:06:29] WARNING: no name column found on line 46 -208: [03:06:29] WARNING: no name column found on line 47 -208: [03:06:29] WARNING: no name column found on line 48 -208: [03:06:29] WARNING: no name column found on line 49 -208: [03:06:29] WARNING: no name column found on line 50 -208: [03:06:29] WARNING: no name column found on line 51 -208: [03:06:29] WARNING: no name column found on line 52 -208: [03:06:29] WARNING: no name column found on line 53 -208: [03:06:29] WARNING: no name column found on line 54 -208: [03:06:29] WARNING: no name column found on line 55 -208: [03:06:29] WARNING: no name column found on line 56 -208: [03:06:29] WARNING: no name column found on line 57 -208: [03:06:29] WARNING: no name column found on line 58 -208: [03:06:29] WARNING: no name column found on line 59 -208: [03:06:29] WARNING: no name column found on line 60 -208: [03:06:29] WARNING: no name column found on line 61 -208: [03:06:29] WARNING: no name column found on line 62 -208: [03:06:29] WARNING: no name column found on line 63 -208: [03:06:29] WARNING: no name column found on line 64 -208: [03:06:29] WARNING: no name column found on line 65 -208: [03:06:29] WARNING: no name column found on line 66 -208: [03:06:29] WARNING: no name column found on line 67 -208: [03:06:29] WARNING: no name column found on line 68 -208: [03:06:29] WARNING: no name column found on line 69 -208: [03:06:29] WARNING: no name column found on line 70 -208: [03:06:29] WARNING: no name column found on line 71 -208: [03:06:29] WARNING: no name column found on line 72 -208: [03:06:29] WARNING: no name column found on line 73 -208: [03:06:29] WARNING: no name column found on line 74 -208: [03:06:29] WARNING: no name column found on line 75 -208: [03:06:29] WARNING: no name column found on line 76 -208: [03:06:29] WARNING: no name column found on line 77 -208: [03:06:29] WARNING: no name column found on line 78 -208: [03:06:29] WARNING: no name column found on line 79 -208: [03:06:29] WARNING: no name column found on line 80 -208: [03:06:29] WARNING: no name column found on line 81 -208: [03:06:29] WARNING: no name column found on line 82 -208: [03:06:29] WARNING: no name column found on line 83 -208: [03:06:29] WARNING: no name column found on line 84 -208: [03:06:29] WARNING: no name column found on line 85 -208: [03:06:29] WARNING: no name column found on line 86 -208: [03:06:29] WARNING: no name column found on line 87 -208: [03:06:29] WARNING: no name column found on line 88 -208: [03:06:29] WARNING: no name column found on line 89 -208: [03:06:29] WARNING: no name column found on line 90 -208: [03:06:29] WARNING: no name column found on line 91 -208: [03:06:29] WARNING: no name column found on line 92 -208: [03:06:29] WARNING: no name column found on line 93 -208: [03:06:29] WARNING: no name column found on line 94 -208: [03:06:29] WARNING: no name column found on line 95 -208: [03:06:29] WARNING: no name column found on line 96 -208: [03:06:29] WARNING: no name column found on line 97 -208: [03:06:29] WARNING: no name column found on line 98 -208: [03:06:29] WARNING: no name column found on line 99 -208: [03:06:29] WARNING: no name column found on line 100 -208: [03:06:29] WARNING: no name column found on line 101 -208: [03:06:29] WARNING: no name column found on line 102 -208: [03:06:29] WARNING: no name column found on line 103 -208: [03:06:29] WARNING: no name column found on line 104 -208: [03:06:29] WARNING: no name column found on line 105 -208: [03:06:29] WARNING: no name column found on line 106 -208: [03:06:29] WARNING: no name column found on line 107 -208: [03:06:29] WARNING: no name column found on line 108 -208: [03:06:29] WARNING: no name column found on line 109 -208: [03:06:29] WARNING: no name column found on line 110 -208: [03:06:29] WARNING: no name column found on line 111 -208: [03:06:29] WARNING: no name column found on line 112 -208: [03:06:29] WARNING: no name column found on line 113 -208: [03:06:29] WARNING: no name column found on line 114 -208: [03:06:29] WARNING: no name column found on line 115 -208: [03:06:29] WARNING: no name column found on line 116 -208: [03:06:29] WARNING: no name column found on line 117 -208: [03:06:29] WARNING: no name column found on line 118 -208: [03:06:29] WARNING: no name column found on line 119 -208: [03:06:29] WARNING: no name column found on line 120 -208: [03:06:29] WARNING: no name column found on line 121 -208: [03:06:29] WARNING: no name column found on line 122 -208: [03:06:29] WARNING: no name column found on line 123 -208: [03:06:29] WARNING: no name column found on line 124 -208: [03:06:29] WARNING: no name column found on line 125 -208: [03:06:29] WARNING: no name column found on line 126 -208: [03:06:29] WARNING: no name column found on line 127 -208: [03:06:29] WARNING: no name column found on line 128 -208: [03:06:29] WARNING: no name column found on line 129 -208: [03:06:29] WARNING: no name column found on line 130 -208: [03:06:29] WARNING: no name column found on line 131 -208: [03:06:29] WARNING: no name column found on line 132 -208: [03:06:29] WARNING: no name column found on line 133 -208: [03:06:29] WARNING: no name column found on line 134 -208: [03:06:29] WARNING: no name column found on line 135 -208: [03:06:29] WARNING: no name column found on line 136 -208: [03:06:29] WARNING: no name column found on line 137 -208: [03:06:29] WARNING: no name column found on line 138 -208: [03:06:29] WARNING: no name column found on line 139 -208: [03:06:29] WARNING: no name column found on line 140 -208: [03:06:29] WARNING: no name column found on line 141 -208: [03:06:29] WARNING: no name column found on line 142 -208: [03:06:29] WARNING: no name column found on line 143 -208: [03:06:29] WARNING: no name column found on line 144 -208: [03:06:29] WARNING: no name column found on line 145 -208: [03:06:29] WARNING: no name column found on line 146 -208: [03:06:29] WARNING: no name column found on line 147 -208: [03:06:29] WARNING: no name column found on line 148 -208: [03:06:29] WARNING: no name column found on line 149 -208: [03:06:29] WARNING: no name column found on line 150 -208: [03:06:29] WARNING: no name column found on line 151 -208: [03:06:29] WARNING: no name column found on line 152 -208: [03:06:29] WARNING: no name column found on line 153 -208: [03:06:29] WARNING: no name column found on line 154 -208: [03:06:29] WARNING: no name column found on line 155 -208: [03:06:29] WARNING: no name column found on line 156 -208: [03:06:29] WARNING: no name column found on line 157 -208: [03:06:29] WARNING: no name column found on line 158 -208: [03:06:29] WARNING: no name column found on line 159 -208: [03:06:29] WARNING: no name column found on line 160 -208: [03:06:29] WARNING: no name column found on line 161 -208: [03:06:29] WARNING: no name column found on line 162 -208: [03:06:29] WARNING: no name column found on line 163 -208: [03:06:29] WARNING: no name column found on line 164 -208: [03:06:29] WARNING: no name column found on line 165 -208: [03:06:29] WARNING: no name column found on line 166 -208: [03:06:29] WARNING: no name column found on line 167 -208: [03:06:29] WARNING: no name column found on line 168 -208: [03:06:29] WARNING: no name column found on line 169 -208: [03:06:29] WARNING: no name column found on line 170 -208: [03:06:29] WARNING: no name column found on line 171 -208: [03:06:29] WARNING: no name column found on line 172 -208: [03:06:29] WARNING: no name column found on line 173 -208: [03:06:29] WARNING: no name column found on line 174 -208: [03:06:29] WARNING: no name column found on line 175 -208: [03:06:29] WARNING: no name column found on line 176 -208: [03:06:29] WARNING: no name column found on line 177 -208: [03:06:29] WARNING: no name column found on line 178 -208: [03:06:29] WARNING: no name column found on line 179 -208: [03:06:29] WARNING: no name column found on line 180 -208: [03:06:29] WARNING: no name column found on line 181 -208: [03:06:29] WARNING: no name column found on line 182 -208: [03:06:29] WARNING: no name column found on line 183 -208: [03:06:29] WARNING: no name column found on line 184 -208: [03:06:29] WARNING: no name column found on line 185 -208: [03:06:29] WARNING: no name column found on line 186 -208: [03:06:29] WARNING: no name column found on line 187 -208: [03:06:29] WARNING: no name column found on line 188 -208: [03:06:29] WARNING: no name column found on line 189 -208: [03:06:29] WARNING: no name column found on line 190 -208: [03:06:29] WARNING: no name column found on line 191 -208: [03:06:29] WARNING: no name column found on line 192 -208: [03:06:29] WARNING: no name column found on line 193 -208: [03:06:29] WARNING: no name column found on line 194 -208: [03:06:29] WARNING: no name column found on line 195 -208: [03:06:29] WARNING: no name column found on line 196 -208: [03:06:29] WARNING: no name column found on line 197 -208: [03:06:29] WARNING: no name column found on line 198 -208: [03:06:29] WARNING: no name column found on line 199 -208: [03:06:29] WARNING: no name column found on line 200 -208: [03:06:29] WARNING: no name column found on line 201 -208: [03:06:29] WARNING: no name column found on line 202 -208: [03:06:29] WARNING: no name column found on line 203 -208: [03:06:29] WARNING: no name column found on line 204 -208: [03:06:29] WARNING: no name column found on line 205 -208: [03:06:29] WARNING: no name column found on line 206 -208: [03:06:29] WARNING: no name column found on line 207 -208: [03:06:29] WARNING: no name column found on line 208 -208: [03:06:29] WARNING: no name column found on line 209 -208: [03:06:29] WARNING: no name column found on line 210 -208: [03:06:29] WARNING: no name column found on line 211 -208: [03:06:29] WARNING: no name column found on line 212 -208: [03:06:29] WARNING: no name column found on line 213 -208: [03:06:29] WARNING: no name column found on line 214 -208: [03:06:29] WARNING: no name column found on line 215 -208: [03:06:29] WARNING: no name column found on line 216 +208: ..[12:13:07] WARNING: not removing hydrogen atom without neighbors +208: .[12:13:07] WARNING: not removing hydrogen atom without neighbors +123: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O +208: .[12:13:07] WARNING: no name column found on line 1 +208: [12:13:07] WARNING: no name column found on line 2 +208: [12:13:07] WARNING: no name column found on line 3 +208: [12:13:07] WARNING: no name column found on line 4 +208: [12:13:07] WARNING: no name column found on line 5 +208: [12:13:07] WARNING: no name column found on line 6 +208: [12:13:07] WARNING: no name column found on line 7 +208: [12:13:07] WARNING: no name column found on line 8 +208: [12:13:07] WARNING: no name column found on line 9 +208: [12:13:07] WARNING: no name column found on line 10 +208: [12:13:07] WARNING: no name column found on line 11 +208: [12:13:07] WARNING: no name column found on line 12 +208: [12:13:07] WARNING: no name column found on line 13 +208: [12:13:07] WARNING: no name column found on line 14 +208: [12:13:07] WARNING: no name column found on line 15 +208: [12:13:07] WARNING: no name column found on line 16 +208: [12:13:07] WARNING: no name column found on line 17 +208: [12:13:07] WARNING: no name column found on line 18 +208: [12:13:07] WARNING: no name column found on line 19 +208: [12:13:07] WARNING: no name column found on line 20 +208: [12:13:07] WARNING: no name column found on line 21 +208: [12:13:07] WARNING: no name column found on line 22 +208: [12:13:07] WARNING: no name column found on line 23 +208: [12:13:07] WARNING: no name column found on line 24 +208: [12:13:07] WARNING: no name column found on line 25 +208: [12:13:07] WARNING: no name column found on line 26 +208: [12:13:07] WARNING: no name column found on line 27 +208: [12:13:07] WARNING: no name column found on line 28 +208: [12:13:07] WARNING: no name column found on line 29 +208: [12:13:07] WARNING: no name column found on line 30 +208: [12:13:07] WARNING: no name column found on line 31 +208: [12:13:07] WARNING: no name column found on line 32 +208: [12:13:07] WARNING: no name column found on line 33 +208: [12:13:07] WARNING: no name column found on line 34 +208: [12:13:07] WARNING: no name column found on line 35 +208: [12:13:07] WARNING: no name column found on line 36 +208: [12:13:07] WARNING: no name column found on line 37 +208: [12:13:07] WARNING: no name column found on line 38 +208: [12:13:07] WARNING: no name column found on line 39 +208: [12:13:07] WARNING: no name column found on line 40 +208: [12:13:07] WARNING: no name column found on line 41 +208: [12:13:07] WARNING: no name column found on line 42 +208: [12:13:07] WARNING: no name column found on line 43 +208: [12:13:07] WARNING: no name column found on line 44 +208: [12:13:07] WARNING: no name column found on line 45 +208: [12:13:07] WARNING: no name column found on line 46 +208: [12:13:07] WARNING: no name column found on line 47 +208: [12:13:07] WARNING: no name column found on line 48 +208: [12:13:07] WARNING: no name column found on line 49 +208: [12:13:07] WARNING: no name column found on line 50 +208: [12:13:07] WARNING: no name column found on line 51 +208: [12:13:07] WARNING: no name column found on line 52 +208: [12:13:07] WARNING: no name column found on line 53 +208: [12:13:07] WARNING: no name column found on line 54 +208: [12:13:07] WARNING: no name column found on line 55 +208: [12:13:07] WARNING: no name column found on line 56 +208: [12:13:07] WARNING: no name column found on line 57 +208: [12:13:07] WARNING: no name column found on line 58 +208: [12:13:07] WARNING: no name column found on line 59 +208: [12:13:07] WARNING: no name column found on line 60 +208: [12:13:07] WARNING: no name column found on line 61 +208: [12:13:07] WARNING: no name column found on line 62 +208: [12:13:07] WARNING: no name column found on line 63 +208: [12:13:07] WARNING: no name column found on line 64 +208: [12:13:07] WARNING: no name column found on line 65 +208: [12:13:07] WARNING: no name column found on line 66 +208: [12:13:07] WARNING: no name column found on line 67 +208: [12:13:07] WARNING: no name column found on line 68 +208: [12:13:07] WARNING: no name column found on line 69 +208: [12:13:07] WARNING: no name column found on line 70 +208: [12:13:07] WARNING: no name column found on line 71 +208: [12:13:07] WARNING: no name column found on line 72 +208: [12:13:07] WARNING: no name column found on line 73 +208: [12:13:07] WARNING: no name column found on line 74 +208: [12:13:07] WARNING: no name column found on line 75 +208: [12:13:07] WARNING: no name column found on line 76 +208: [12:13:07] WARNING: no name column found on line 77 +208: [12:13:07] WARNING: no name column found on line 78 +208: [12:13:07] WARNING: no name column found on line 79 +208: [12:13:07] WARNING: no name column found on line 80 +208: [12:13:07] WARNING: no name column found on line 81 +208: [12:13:07] WARNING: no name column found on line 82 +208: [12:13:07] WARNING: no name column found on line 83 +208: [12:13:07] WARNING: no name column found on line 84 +208: [12:13:07] WARNING: no name column found on line 85 +208: [12:13:07] WARNING: no name column found on line 86 +208: [12:13:07] WARNING: no name column found on line 87 +208: [12:13:07] WARNING: no name column found on line 88 +208: [12:13:07] WARNING: no name column found on line 89 +208: [12:13:07] WARNING: no name column found on line 90 +208: [12:13:07] WARNING: no name column found on line 91 +208: [12:13:07] WARNING: no name column found on line 92 +208: [12:13:07] WARNING: no name column found on line 93 +208: [12:13:07] WARNING: no name column found on line 94 +208: [12:13:07] WARNING: no name column found on line 95 +208: [12:13:07] WARNING: no name column found on line 96 +208: [12:13:07] WARNING: no name column found on line 97 +208: [12:13:07] WARNING: no name column found on line 98 +208: [12:13:07] WARNING: no name column found on line 99 +208: [12:13:07] WARNING: no name column found on line 100 +208: [12:13:07] WARNING: no name column found on line 101 +208: [12:13:07] WARNING: no name column found on line 102 +208: [12:13:07] WARNING: no name column found on line 103 +208: [12:13:07] WARNING: no name column found on line 104 +208: [12:13:07] WARNING: no name column found on line 105 +208: [12:13:07] WARNING: no name column found on line 106 +208: [12:13:07] WARNING: no name column found on line 107 +208: [12:13:07] WARNING: no name column found on line 108 +208: [12:13:07] WARNING: no name column found on line 109 +208: [12:13:07] WARNING: no name column found on line 110 +208: [12:13:07] WARNING: no name column found on line 111 +208: [12:13:07] WARNING: no name column found on line 112 +208: [12:13:07] WARNING: no name column found on line 113 +208: [12:13:07] WARNING: no name column found on line 114 +208: [12:13:07] WARNING: no name column found on line 115 +208: [12:13:07] WARNING: no name column found on line 116 +208: [12:13:07] WARNING: no name column found on line 117 +208: [12:13:07] WARNING: no name column found on line 118 +208: [12:13:07] WARNING: no name column found on line 119 +208: [12:13:07] WARNING: no name column found on line 120 +208: [12:13:07] WARNING: no name column found on line 121 +208: [12:13:07] WARNING: no name column found on line 122 +208: [12:13:07] WARNING: no name column found on line 123 +208: [12:13:07] WARNING: no name column found on line 124 +208: [12:13:07] WARNING: no name column found on line 125 +208: [12:13:07] WARNING: no name column found on line 126 +208: [12:13:07] WARNING: no name column found on line 127 +208: [12:13:07] WARNING: no name column found on line 128 +208: [12:13:07] WARNING: no name column found on line 129 +208: [12:13:07] WARNING: no name column found on line 130 +208: [12:13:07] WARNING: no name column found on line 131 +208: [12:13:07] WARNING: no name column found on line 132 +208: [12:13:07] WARNING: no name column found on line 133 +208: [12:13:07] WARNING: no name column found on line 134 +208: [12:13:07] WARNING: no name column found on line 135 +208: [12:13:07] WARNING: no name column found on line 136 +208: [12:13:07] WARNING: no name column found on line 137 +208: [12:13:07] WARNING: no name column found on line 138 +208: [12:13:07] WARNING: no name column found on line 139 +208: [12:13:07] WARNING: no name column found on line 140 +208: [12:13:07] WARNING: no name column found on line 141 +208: [12:13:07] WARNING: no name column found on line 142 +208: [12:13:07] WARNING: no name column found on line 143 +208: [12:13:07] WARNING: no name column found on line 144 +208: [12:13:07] WARNING: no name column found on line 145 +208: [12:13:07] WARNING: no name column found on line 146 +208: [12:13:07] WARNING: no name column found on line 147 +208: [12:13:07] WARNING: no name column found on line 148 +208: [12:13:07] WARNING: no name column found on line 149 +208: [12:13:07] WARNING: no name column found on line 150 +208: [12:13:07] WARNING: no name column found on line 151 +208: [12:13:07] WARNING: no name column found on line 152 +208: [12:13:07] WARNING: no name column found on line 153 +208: [12:13:07] WARNING: no name column found on line 154 +208: [12:13:07] WARNING: no name column found on line 155 +208: [12:13:07] WARNING: no name column found on line 156 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173 +208: [12:13:07] WARNING: no name column found on line 174 +208: [12:13:07] WARNING: no name column found on line 175 +208: [12:13:07] WARNING: no name column found on line 176 +208: [12:13:07] WARNING: no name column found on line 177 +208: [12:13:07] WARNING: no name column found on line 178 +208: [12:13:07] WARNING: no name column found on line 179 +208: [12:13:07] WARNING: no name column found on line 180 +208: [12:13:07] WARNING: no name column found on line 181 +208: [12:13:07] WARNING: no name column found on line 182 +208: [12:13:07] WARNING: no name column found on line 183 +208: [12:13:07] WARNING: no name column found on line 184 +208: [12:13:07] WARNING: no name column found on line 185 +208: [12:13:07] WARNING: no name column found on line 186 +208: [12:13:07] WARNING: no name column found on line 187 +208: [12:13:07] WARNING: no name column found on line 188 +208: [12:13:07] WARNING: no name column found on line 189 +208: [12:13:07] WARNING: no name column found on line 190 +208: [12:13:07] WARNING: no name column found on line 191 +208: [12:13:07] WARNING: no name column found on line 192 +208: [12:13:07] WARNING: no name column found on line 193 +208: [12:13:07] WARNING: no name column found on line 194 +208: [12:13:07] WARNING: no name column found on line 195 +208: [12:13:07] WARNING: no name column found on line 196 +208: [12:13:07] WARNING: no name column found on line 197 +208: [12:13:07] WARNING: no name column found on line 198 +208: [12:13:07] WARNING: no name column found on line 199 +208: [12:13:07] WARNING: no name column found on line 200 +208: [12:13:07] WARNING: no name column found on line 201 +208: [12:13:07] WARNING: no name column found on line 202 +208: [12:13:07] WARNING: no name column found on line 203 +208: [12:13:07] WARNING: no name column found on line 204 +208: [12:13:07] WARNING: no name column found on line 205 +208: [12:13:07] WARNING: no name column found on line 206 +208: [12:13:07] WARNING: no name column found on line 207 +208: [12:13:07] WARNING: no name column found on line 208 +208: [12:13:07] WARNING: no name column found on line 209 +208: [12:13:07] WARNING: no name column found on line 210 +208: [12:13:07] WARNING: no name column found on line 211 +208: [12:13:07] WARNING: no name column found on line 212 +208: [12:13:07] WARNING: no name column found on line 213 +208: [12:13:07] WARNING: no name column found on line 214 +208: [12:13:07] WARNING: no name column found on line 215 +208: [12:13:07] WARNING: no name column found on line 216 208: ...... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.152s +208: Ran 10 tests in 0.182s 208: 208: OK +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 +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 208: .................. 208: ---------------------------------------------------------------------- -208: Ran 18 tests in 0.946s +208: Ran 18 tests in 1.210s 208: 208: OK -123: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 +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: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.103s +208: Ran 3 tests in 0.121s 208: 208: OK -123: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 208: ........ 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.039s +208: Ran 8 tests in 0.053s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.029s +208: Ran 2 tests in 0.030s 208: 208: OK -123: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.018s +208: Ran 2 tests in 0.022s 208: 208: OK -123: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 208: . 208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.082s +208: Ran 1 test in 0.100s 208: 208: OK +123: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 208: ........ 208: ---------------------------------------------------------------------- 208: Ran 8 tests in 0.002s 208: 208: OK +123: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 208: ... 208: ---------------------------------------------------------------------- 208: Ran 3 tests in 0.006s @@ -31686,6 +31720,7 @@ 208: Ran 3 tests in 0.002s 208: 208: OK +123: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 208: ...E 208: ====================================================================== 208: ERROR: test_CombineFeatMaps (__main__.TestCase.test_CombineFeatMaps) @@ -31705,32 +31740,32 @@ 208: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 208: 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.006s +208: Ran 4 tests in 0.009s 208: 208: FAILED (errors=1) -123: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 208: !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} +123: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 208: ....... 208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.020s +208: Ran 7 tests in 0.019s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.024s +208: Ran 4 tests in 0.025s 208: 208: OK +123: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 123: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 123: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -123: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 3.499s +208: Ran 4 tests in 3.847s 208: 208: OK 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.067s +208: Ran 10 tests in 0.069s 208: 208: OK 208: . @@ -31738,10 +31773,10 @@ 208: Ran 1 test in 0.000s 208: 208: OK -123: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 +123: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.005s +208: Ran 10 tests in 0.006s 208: 208: OK 208: ....E @@ -31760,22 +31795,21 @@ 208: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 208: 208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.081s +208: Ran 5 tests in 0.065s 208: 208: FAILED (errors=1) 208: !!! TEST FAILURE: python UnitTestGobbi.py {} +123: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 123: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 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 -208: ................[03:06:51] Molecule does not have explicit Hs. Consider calling AddHs() -208: [03:06:51] Molecule does not have explicit Hs. Consider calling AddHs() +208: ................[12:13:33] Molecule does not have explicit Hs. Consider calling AddHs() +208: [12:13:33] Molecule does not have explicit Hs. Consider calling AddHs() 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 21 tests in 8.790s +208: Ran 21 tests in 10.088s 208: 208: OK 208: mol_197 @@ -31789,7 +31823,8 @@ 208: Ran 1 test in 0.000s 208: 208: OK -208: ...[03:06:52] +123: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 +208: ...[12:13:33] 208: 208: **** 208: Pre-condition Violation @@ -31800,71 +31835,68 @@ 208: 208: . 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.030s +208: Ran 4 tests in 0.032s 208: 208: OK +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-] -5: [03:06:57] Finished: testMultipleTimes() -5: [03:06:57] -5: ----------------------------------------- -206/208 Test #5: testConcurrentQueue .................... Passed 167.15 sec 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 8.316s +208: Ran 2 tests in 9.591s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.103s +208: Ran 2 tests in 0.153s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.014s +208: Ran 3 tests in 0.018s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.022s +208: Ran 4 tests in 0.037s 208: 208: OK -208: .....[03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors -208: [03:07:03] WARNING: not removing hydrogen atom without neighbors +208: .....[12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors +208: [12:13:46] WARNING: not removing hydrogen atom without neighbors 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.372s +208: Ran 10 tests in 0.499s 208: 208: OK -208: ssssss[03:07:04] No suitable metadata found. -208: .[03:07:04] No suitable metadata found. +208: ssssss[12:13:48] No suitable metadata found. +208: .[12:13:48] No suitable metadata found. 208: ......s/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/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 0.452s +208: Ran 19 tests in 0.700s 208: 208: OK (skipped=7) 208: sss. 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.942s +208: Ran 4 tests in 1.138s 208: 208: OK (skipped=3) 208: sss @@ -31872,37 +31904,37 @@ 208: Ran 3 tests in 0.000s 208: 208: OK (skipped=3) -123: [03:07:06] Molecule does not have explicit Hs. Consider calling AddHs() -207/208 Test #123: testDistGeomHelpers .................... Passed 166.09 sec 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.579s +208: Ran 10 tests in 0.959s 208: 208: OK -208: ..[03:07:07] SMARTS Parse Error: syntax error while parsing: boromicacid -208: [03:07:07] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -208: [03:07:07] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -208: [03:07:07] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -208: [03:07:07] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -208: [03:07:07] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -208: [03:07:07] reaction has no reactants -208: [03:07:07] reaction has no products -208: [03:07:07] initialization failed -208: [03:07:07] reaction has no reactants -208: [03:07:07] reaction has no products +123: [12:13:52] Molecule does not have explicit Hs. Consider calling AddHs() +206/208 Test #123: testDistGeomHelpers .................... Passed 205.01 sec +208: ..[12:13:53] SMARTS Parse Error: syntax error while parsing: boromicacid +208: [12:13:53] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +208: [12:13:53] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +208: [12:13:53] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +208: [12:13:53] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +208: [12:13:53] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +208: [12:13:53] reaction has no reactants +208: [12:13:53] reaction has no products +208: [12:13:53] initialization failed +208: [12:13:53] reaction has no reactants +208: [12:13:53] reaction has no products 208: . 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.030s +208: Ran 3 tests in 0.042s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.013s +208: Ran 4 tests in 0.015s 208: 208: OK 208: .................... 208: ---------------------------------------------------------------------- -208: Ran 20 tests in 0.103s +208: Ran 20 tests in 0.134s 208: 208: OK 208: !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} @@ -31911,18 +31943,18 @@ 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 138.96 sec +207/208 Test #208: pythonTestDirChem ......................***Failed 174.46 sec ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.099s +Ran 7 tests in 0.238s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.082s +Ran 6 tests in 0.110s OK -....[03:04:51] +....[12:11:03] **** Pre-condition Violation @@ -31933,22 +31965,22 @@ . ---------------------------------------------------------------------- -Ran 5 tests in 0.010s +Ran 5 tests in 0.031s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.010s +Ran 4 tests in 0.034s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.014s +Ran 2 tests in 0.026s OK ...................... ---------------------------------------------------------------------- -Ran 22 tests in 0.039s +Ran 22 tests in 0.042s OK .....s..........E......ss @@ -31973,60 +32005,60 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 25 tests in 0.155s +Ran 25 tests in 0.336s FAILED (errors=1, skipped=3) ..s ---------------------------------------------------------------------- -Ran 3 tests in 0.199s +Ran 3 tests in 0.411s OK (skipped=1) ................................... ---------------------------------------------------------------------- -Ran 35 tests in 1.062s +Ran 35 tests in 1.101s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.042s +Ran 4 tests in 0.026s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.017s +Ran 1 test in 0.026s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.076s +Ran 7 tests in 0.115s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.061s +Ran 3 tests in 0.118s OK .ss.ss....... ---------------------------------------------------------------------- -Ran 13 tests in 1.192s +Ran 13 tests in 2.731s OK (skipped=4) -[03:04:59] Molecule does not have explicit Hs. Consider calling AddHs() -.[03:04:59] Molecule does not have explicit Hs. Consider calling AddHs() -..................[03:05:51] WARNING: More than one matching pattern found - picking one +[12:11:16] Molecule does not have explicit Hs. Consider calling AddHs() +.[12:11:16] Molecule does not have explicit Hs. Consider calling AddHs() +..................[12:12:21] WARNING: More than one matching pattern found - picking one -[03:05:51] WARNING: More than one matching pattern found - picking one +[12:12:21] WARNING: More than one matching pattern found - picking one -.[03:05:51] WARNING: More than one matching pattern found - picking one +.[12:12:21] WARNING: More than one matching pattern found - picking one ... ---------------------------------------------------------------------- -Ran 23 tests in 57.684s +Ran 23 tests in 71.041s OK -{'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) @@ -32046,7 +32078,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 8 tests in 0.122s +Ran 8 tests in 0.158s FAILED (errors=1) Traceback (most recent call last): @@ -32081,10 +32113,10 @@ `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..[03:06:02] WARNING: not removing hydrogen atom without neighbors -[03:06:02] WARNING: not removing hydrogen atom without neighbors -[03:06:02] WARNING: not removing hydrogen atom without neighbors -....[03:06:02] WARNING: not removing hydrogen atom without neighbors +F..[12:12:33] WARNING: not removing hydrogen atom without neighbors +[12:12:33] WARNING: not removing hydrogen atom without neighbors +[12:12:33] WARNING: not removing hydrogen atom without neighbors +....[12:12:33] WARNING: not removing hydrogen atom without neighbors ...... ====================================================================== FAIL: testBadAtomHandling (__main__.TestCase.testBadAtomHandling) @@ -32141,17 +32173,17 @@ AssertionError: SMILES: CCC; Descriptor: Ipc ---------------------------------------------------------------------- -Ran 14 tests in 4.585s +Ran 14 tests in 4.964s FAILED (failures=2) .... ---------------------------------------------------------------------- -Ran 4 tests in 2.455s +Ran 4 tests in 1.775s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.368s +Ran 6 tests in 0.393s OK .......:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. @@ -32162,17 +32194,17 @@ antibiotics = antibiotics.append({ .......s..s........ ---------------------------------------------------------------------- -Ran 26 tests in 3.095s +Ran 26 tests in 4.328s OK (skipped=2) -.............F[03:06:27] WARNING: More than one matching pattern found - picking one +.............F[12:13:04] WARNING: More than one matching pattern found - picking one -[03:06:27] WARNING: More than one matching pattern found - picking one +[12:13:04] WARNING: More than one matching pattern found - picking one -..[03:06:27] Molecule does not have explicit Hs. Consider calling AddHs() -[03:06:27] Molecule does not have explicit Hs. Consider calling AddHs() -[03:06:27] Molecule does not have explicit Hs. Consider calling AddHs() -[03:06:27] Molecule does not have explicit Hs. Consider calling AddHs() +..[12:13:04] Molecule does not have explicit Hs. Consider calling AddHs() +[12:13:04] Molecule does not have explicit Hs. Consider calling AddHs() +[12:13:04] Molecule does not have explicit Hs. Consider calling AddHs() +[12:13:04] Molecule does not have explicit Hs. Consider calling AddHs() ......... ====================================================================== FAIL: FindBRICSBonds (rdkit.Chem.BRICS) @@ -32201,270 +32233,270 @@ ---------------------------------------------------------------------- -Ran 25 tests in 15.528s +Ran 25 tests in 19.665s FAILED (failures=1) .. ---------------------------------------------------------------------- -Ran 2 tests in 0.067s +Ran 2 tests in 0.070s OK ..s... ---------------------------------------------------------------------- -Ran 6 tests in 0.960s +Ran 6 tests in 1.374s OK (skipped=1) -..[03:06:29] WARNING: not removing hydrogen atom without neighbors -.[03:06:29] WARNING: not removing hydrogen atom without neighbors -.[03:06:29] WARNING: no name column found on line 1 -[03:06:29] WARNING: no name column found on line 2 -[03:06:29] WARNING: no name column found on line 3 -[03:06:29] WARNING: no name column found on line 4 -[03:06:29] WARNING: no name column found on line 5 -[03:06:29] WARNING: no name column found on line 6 -[03:06:29] WARNING: no name column found on line 7 -[03:06:29] WARNING: no name column found on line 8 -[03:06:29] WARNING: no name column found on line 9 -[03:06:29] WARNING: no name column found on line 10 -[03:06:29] WARNING: no name column found on line 11 -[03:06:29] WARNING: no name column found on line 12 -[03:06:29] WARNING: no name column found on line 13 -[03:06:29] WARNING: no name column found on line 14 -[03:06:29] WARNING: no name column found on line 15 -[03:06:29] WARNING: no name column found on line 16 -[03:06:29] WARNING: no name column found on line 17 -[03:06:29] WARNING: no name column found on line 18 -[03:06:29] WARNING: no name column found on line 19 -[03:06:29] WARNING: no name column found on line 20 -[03:06:29] WARNING: no name column found on line 21 -[03:06:29] WARNING: no name column found on line 22 -[03:06:29] WARNING: no name column found on line 23 -[03:06:29] WARNING: no name column found on line 24 -[03:06:29] WARNING: no name column found on line 25 -[03:06:29] WARNING: no name column found on line 26 -[03:06:29] WARNING: no name column found on line 27 -[03:06:29] WARNING: no name column found on line 28 -[03:06:29] WARNING: no name column found on line 29 -[03:06:29] WARNING: no name column found on line 30 -[03:06:29] WARNING: no name column found on line 31 -[03:06:29] WARNING: no name column found on line 32 -[03:06:29] WARNING: no name column found on line 33 -[03:06:29] WARNING: no name column found on line 34 -[03:06:29] WARNING: no name column found on line 35 -[03:06:29] WARNING: no name column found on line 36 -[03:06:29] WARNING: no name column found on line 37 -[03:06:29] WARNING: no name column found on line 38 -[03:06:29] WARNING: no name column found on line 39 -[03:06:29] WARNING: no name column found on line 40 -[03:06:29] WARNING: no name column found on line 41 -[03:06:29] WARNING: no name column found on line 42 -[03:06:29] WARNING: no name column found on line 43 -[03:06:29] WARNING: no name column found on line 44 -[03:06:29] WARNING: no name column found on line 45 -[03:06:29] WARNING: no name column found on line 46 -[03:06:29] WARNING: no name column found on line 47 -[03:06:29] WARNING: no name column found on line 48 -[03:06:29] WARNING: no name column found on line 49 -[03:06:29] WARNING: no name column found on line 50 -[03:06:29] WARNING: no name column found on line 51 -[03:06:29] WARNING: no name column found on line 52 -[03:06:29] WARNING: no name column found on line 53 -[03:06:29] WARNING: no name column found on line 54 -[03:06:29] WARNING: no name column found on line 55 -[03:06:29] WARNING: no name column found on line 56 -[03:06:29] WARNING: no name column found on line 57 -[03:06:29] WARNING: no name column found on line 58 -[03:06:29] WARNING: no name column found on line 59 -[03:06:29] WARNING: no name column found on line 60 -[03:06:29] WARNING: no name column found on line 61 -[03:06:29] WARNING: no name column found on line 62 -[03:06:29] WARNING: no name column found on line 63 -[03:06:29] WARNING: no name column found on line 64 -[03:06:29] WARNING: no name column found on line 65 -[03:06:29] WARNING: no name column found on line 66 -[03:06:29] WARNING: no name column found on line 67 -[03:06:29] WARNING: no name column found on line 68 -[03:06:29] WARNING: no name column found on line 69 -[03:06:29] WARNING: no name column found on line 70 -[03:06:29] WARNING: no name column found on line 71 -[03:06:29] WARNING: no name column found on line 72 -[03:06:29] WARNING: no name column found on line 73 -[03:06:29] WARNING: no name column found on line 74 -[03:06:29] WARNING: no name column found on line 75 -[03:06:29] WARNING: no name column found on line 76 -[03:06:29] WARNING: no name column found on line 77 -[03:06:29] WARNING: no name column found on line 78 -[03:06:29] WARNING: no name column found on line 79 -[03:06:29] WARNING: no name column found on line 80 -[03:06:29] WARNING: no name column found on line 81 -[03:06:29] WARNING: no name column found on line 82 -[03:06:29] WARNING: no name column found on line 83 -[03:06:29] WARNING: no name column found on line 84 -[03:06:29] WARNING: no name column found on line 85 -[03:06:29] WARNING: no name column found on line 86 -[03:06:29] WARNING: no name column found on line 87 -[03:06:29] WARNING: no name column found on line 88 -[03:06:29] WARNING: no name column found on line 89 -[03:06:29] WARNING: no name column found on line 90 -[03:06:29] WARNING: no name column found on line 91 -[03:06:29] WARNING: no name column found on line 92 -[03:06:29] WARNING: no name column found on line 93 -[03:06:29] WARNING: no name column found on line 94 -[03:06:29] WARNING: no name column found on line 95 -[03:06:29] WARNING: no name column found on line 96 -[03:06:29] WARNING: no name column found on line 97 -[03:06:29] WARNING: no name column found on line 98 -[03:06:29] WARNING: no name column found on line 99 -[03:06:29] WARNING: no name column found on line 100 -[03:06:29] WARNING: no name column found on line 101 -[03:06:29] WARNING: no name column found on line 102 -[03:06:29] WARNING: no name column found on line 103 -[03:06:29] WARNING: no name column found on line 104 -[03:06:29] WARNING: no name column found on line 105 -[03:06:29] WARNING: no name column found on line 106 -[03:06:29] WARNING: no name column found on line 107 -[03:06:29] WARNING: no name column found on line 108 -[03:06:29] WARNING: no name column found on line 109 -[03:06:29] WARNING: no name column found on line 110 -[03:06:29] WARNING: no name column found on line 111 -[03:06:29] WARNING: no name column found on line 112 -[03:06:29] WARNING: no name column found on line 113 -[03:06:29] WARNING: no name column found on line 114 -[03:06:29] WARNING: no name column found on line 115 -[03:06:29] WARNING: no name column found on line 116 -[03:06:29] WARNING: no name column found on line 117 -[03:06:29] WARNING: no name column found on line 118 -[03:06:29] WARNING: no name column found on line 119 -[03:06:29] WARNING: no name column found on line 120 -[03:06:29] WARNING: no name column found on line 121 -[03:06:29] WARNING: no name column found on line 122 -[03:06:29] WARNING: no name column found on line 123 -[03:06:29] WARNING: no name column found on line 124 -[03:06:29] WARNING: no name column found on line 125 -[03:06:29] WARNING: no name column found on line 126 -[03:06:29] WARNING: no name column found on line 127 -[03:06:29] WARNING: no name column found on line 128 -[03:06:29] WARNING: no name column found on line 129 -[03:06:29] WARNING: no name column found on line 130 -[03:06:29] WARNING: no name column found on line 131 -[03:06:29] WARNING: no name column found on line 132 -[03:06:29] WARNING: no name column found on line 133 -[03:06:29] WARNING: no name column found on line 134 -[03:06:29] WARNING: no name column found on line 135 -[03:06:29] WARNING: no name column found on line 136 -[03:06:29] WARNING: no name column found on line 137 -[03:06:29] WARNING: no name column found on line 138 -[03:06:29] WARNING: no name column found on line 139 -[03:06:29] WARNING: no name column found on line 140 -[03:06:29] WARNING: no name column found on line 141 -[03:06:29] WARNING: no name column found on line 142 -[03:06:29] WARNING: no name column found on line 143 -[03:06:29] WARNING: no name column found on line 144 -[03:06:29] WARNING: no name column found on line 145 -[03:06:29] WARNING: no name column found on line 146 -[03:06:29] WARNING: no name column found on line 147 -[03:06:29] WARNING: no name column found on line 148 -[03:06:29] WARNING: no name column found on line 149 -[03:06:29] WARNING: no name column found on line 150 -[03:06:29] WARNING: no name column found on line 151 -[03:06:29] WARNING: no name column found on line 152 -[03:06:29] WARNING: no name column found on line 153 -[03:06:29] WARNING: no name column found on line 154 -[03:06:29] WARNING: no name column found on line 155 -[03:06:29] WARNING: no name column found on line 156 -[03:06:29] WARNING: no name column found on line 157 -[03:06:29] WARNING: no name column found on line 158 -[03:06:29] WARNING: no name column found on line 159 -[03:06:29] WARNING: no name column found on line 160 -[03:06:29] WARNING: no name column found on line 161 -[03:06:29] WARNING: no name column found on line 162 -[03:06:29] WARNING: no name column found on line 163 -[03:06:29] WARNING: no name column found on line 164 -[03:06:29] WARNING: no name column found on line 165 -[03:06:29] WARNING: no name column found on line 166 -[03:06:29] WARNING: no name column found on line 167 -[03:06:29] WARNING: no name column found on line 168 -[03:06:29] WARNING: no name column found on line 169 -[03:06:29] WARNING: no name column found on line 170 -[03:06:29] WARNING: no name column found on line 171 -[03:06:29] WARNING: no name column found on line 172 -[03:06:29] WARNING: no name column found on line 173 -[03:06:29] WARNING: no name column found on line 174 -[03:06:29] WARNING: no name column found on line 175 -[03:06:29] WARNING: no name column found on line 176 -[03:06:29] WARNING: no name column found on line 177 -[03:06:29] WARNING: no name column found on line 178 -[03:06:29] WARNING: no name column found on line 179 -[03:06:29] WARNING: no name column found on line 180 -[03:06:29] WARNING: no name column found on line 181 -[03:06:29] WARNING: no name column found on line 182 -[03:06:29] WARNING: no name column found on line 183 -[03:06:29] WARNING: no name column found on line 184 -[03:06:29] WARNING: no name column found on line 185 -[03:06:29] WARNING: no name column found on line 186 -[03:06:29] WARNING: no name column found on line 187 -[03:06:29] WARNING: no name column found on line 188 -[03:06:29] WARNING: no name column found on line 189 -[03:06:29] WARNING: no name column found on line 190 -[03:06:29] WARNING: no name column found on line 191 -[03:06:29] WARNING: no name column found on line 192 -[03:06:29] WARNING: no name column found on line 193 -[03:06:29] WARNING: no name column found on line 194 -[03:06:29] WARNING: no name column found on line 195 -[03:06:29] WARNING: no name column found on line 196 -[03:06:29] WARNING: no name column found on line 197 -[03:06:29] WARNING: no name column found on line 198 -[03:06:29] WARNING: no name column found on line 199 -[03:06:29] WARNING: no name column found on line 200 -[03:06:29] WARNING: no name column found on line 201 -[03:06:29] WARNING: no name column found on line 202 -[03:06:29] WARNING: no name column found on line 203 -[03:06:29] WARNING: no name column found on line 204 -[03:06:29] WARNING: no name column found on line 205 -[03:06:29] WARNING: no name column found on line 206 -[03:06:29] WARNING: no name column found on line 207 -[03:06:29] WARNING: no name column found on line 208 -[03:06:29] WARNING: no name column found on line 209 -[03:06:29] WARNING: no name column found on line 210 -[03:06:29] WARNING: no name column found on line 211 -[03:06:29] WARNING: no name column found on line 212 -[03:06:29] WARNING: no name column found on line 213 -[03:06:29] WARNING: no name column found on line 214 -[03:06:29] WARNING: no name column found on line 215 -[03:06:29] WARNING: no name column found on line 216 +..[12:13:07] WARNING: not removing hydrogen atom without neighbors +.[12:13:07] WARNING: not removing hydrogen atom without neighbors +.[12:13:07] WARNING: no name column found on line 1 +[12:13:07] WARNING: no name column found on line 2 +[12:13:07] WARNING: no name column found on line 3 +[12:13:07] WARNING: no name column found on line 4 +[12:13:07] WARNING: no name column found on line 5 +[12:13:07] WARNING: no name column found on line 6 +[12:13:07] WARNING: no name column found on line 7 +[12:13:07] WARNING: no name column found on line 8 +[12:13:07] WARNING: no name column found on line 9 +[12:13:07] WARNING: no name column found on line 10 +[12:13:07] WARNING: no name column found on line 11 +[12:13:07] WARNING: no name column found on line 12 +[12:13:07] WARNING: no name column found on line 13 +[12:13:07] WARNING: no name column found on line 14 +[12:13:07] WARNING: no name column found on line 15 +[12:13:07] WARNING: no name column found on line 16 +[12:13:07] WARNING: no name column found on line 17 +[12:13:07] WARNING: no name column found on line 18 +[12:13:07] WARNING: no name column found on line 19 +[12:13:07] WARNING: no name column found on line 20 +[12:13:07] WARNING: no name column found on line 21 +[12:13:07] WARNING: no name column found on line 22 +[12:13:07] WARNING: no name column found on line 23 +[12:13:07] WARNING: no name column found on line 24 +[12:13:07] WARNING: no name column found on line 25 +[12:13:07] WARNING: no name column found on line 26 +[12:13:07] WARNING: no name column found on line 27 +[12:13:07] WARNING: no name column found on line 28 +[12:13:07] WARNING: no name column found on line 29 +[12:13:07] WARNING: no name column found on line 30 +[12:13:07] WARNING: no name column found on line 31 +[12:13:07] WARNING: no name column found on line 32 +[12:13:07] WARNING: no name column found on line 33 +[12:13:07] WARNING: no name column found on line 34 +[12:13:07] WARNING: no name column found on line 35 +[12:13:07] WARNING: no name column found on line 36 +[12:13:07] WARNING: no name column found on line 37 +[12:13:07] WARNING: no name column found on line 38 +[12:13:07] WARNING: no name column found on line 39 +[12:13:07] WARNING: no name column found on line 40 +[12:13:07] WARNING: no name column found on line 41 +[12:13:07] WARNING: no name column found on line 42 +[12:13:07] WARNING: no name column found on line 43 +[12:13:07] WARNING: no name column found on line 44 +[12:13:07] WARNING: no name column found on line 45 +[12:13:07] WARNING: no name column found on line 46 +[12:13:07] WARNING: no name column found on line 47 +[12:13:07] WARNING: no name column found on line 48 +[12:13:07] WARNING: no name column found on line 49 +[12:13:07] WARNING: no name column found on line 50 +[12:13:07] WARNING: no name column found on line 51 +[12:13:07] WARNING: no name column found on line 52 +[12:13:07] WARNING: no name column found on line 53 +[12:13:07] WARNING: no name column found on line 54 +[12:13:07] WARNING: no name column found on line 55 +[12:13:07] WARNING: no name column found on line 56 +[12:13:07] WARNING: no name column found on line 57 +[12:13:07] WARNING: no name column found on line 58 +[12:13:07] WARNING: no name column found on line 59 +[12:13:07] WARNING: no name column found on line 60 +[12:13:07] WARNING: no name column found on line 61 +[12:13:07] WARNING: no name column found on line 62 +[12:13:07] WARNING: no name column found on line 63 +[12:13:07] WARNING: no name column found on line 64 +[12:13:07] WARNING: no name column found on line 65 +[12:13:07] WARNING: no name column found on line 66 +[12:13:07] WARNING: no name column found on line 67 +[12:13:07] WARNING: no name column found on line 68 +[12:13:07] WARNING: no name column found on line 69 +[12:13:07] WARNING: no name column found on line 70 +[12:13:07] WARNING: no name column found on line 71 +[12:13:07] WARNING: no name column found on line 72 +[12:13:07] WARNING: no name column found on line 73 +[12:13:07] WARNING: no name column found on line 74 +[12:13:07] WARNING: no name column found on line 75 +[12:13:07] WARNING: no name column found on line 76 +[12:13:07] WARNING: no name column found on line 77 +[12:13:07] WARNING: no name column found on line 78 +[12:13:07] WARNING: no name column found on line 79 +[12:13:07] WARNING: no name column found on line 80 +[12:13:07] WARNING: no name column found on line 81 +[12:13:07] WARNING: no name column found on line 82 +[12:13:07] WARNING: no name column found on line 83 +[12:13:07] WARNING: no name column found on line 84 +[12:13:07] WARNING: no name column found on line 85 +[12:13:07] WARNING: no name column found on line 86 +[12:13:07] WARNING: no name column found on line 87 +[12:13:07] WARNING: no name column found on line 88 +[12:13:07] WARNING: no name column found on line 89 +[12:13:07] WARNING: no name column found on line 90 +[12:13:07] WARNING: no name column found on line 91 +[12:13:07] WARNING: no name column found on line 92 +[12:13:07] WARNING: no name column found on line 93 +[12:13:07] WARNING: no name column found on line 94 +[12:13:07] WARNING: no name column found on line 95 +[12:13:07] WARNING: no name column found on line 96 +[12:13:07] WARNING: no name column found on line 97 +[12:13:07] WARNING: no name column found on line 98 +[12:13:07] WARNING: no name column found on line 99 +[12:13:07] WARNING: no name column found on line 100 +[12:13:07] WARNING: no name column found on line 101 +[12:13:07] WARNING: no name column found on line 102 +[12:13:07] WARNING: no name column found on line 103 +[12:13:07] WARNING: no name column found on line 104 +[12:13:07] WARNING: no name column found on line 105 +[12:13:07] WARNING: no name column found on line 106 +[12:13:07] WARNING: no name column found on line 107 +[12:13:07] WARNING: no name column found on line 108 +[12:13:07] WARNING: no name column found on line 109 +[12:13:07] WARNING: no name column found on line 110 +[12:13:07] WARNING: no name column found on line 111 +[12:13:07] WARNING: no name column found on line 112 +[12:13:07] WARNING: no name column found on line 113 +[12:13:07] WARNING: no name column found on line 114 +[12:13:07] WARNING: no name column found on line 115 +[12:13:07] WARNING: no name column found on line 116 +[12:13:07] WARNING: no name column found on line 117 +[12:13:07] WARNING: no name column found on line 118 +[12:13:07] WARNING: no name column found on line 119 +[12:13:07] WARNING: no name column found on line 120 +[12:13:07] WARNING: no name column found on line 121 +[12:13:07] WARNING: no name column found on line 122 +[12:13:07] WARNING: no name column found on line 123 +[12:13:07] WARNING: no name column found on line 124 +[12:13:07] WARNING: no name column found on line 125 +[12:13:07] WARNING: no name column found on line 126 +[12:13:07] WARNING: no name column found on line 127 +[12:13:07] WARNING: no name column found on line 128 +[12:13:07] WARNING: no name column found on line 129 +[12:13:07] WARNING: no name column found on line 130 +[12:13:07] WARNING: no name column found on line 131 +[12:13:07] WARNING: no name column found on line 132 +[12:13:07] WARNING: no name column found on line 133 +[12:13:07] WARNING: no name column found on line 134 +[12:13:07] WARNING: no name column found on line 135 +[12:13:07] WARNING: no name column found on line 136 +[12:13:07] WARNING: no name column found on line 137 +[12:13:07] WARNING: no name column found on line 138 +[12:13:07] WARNING: no name column found on line 139 +[12:13:07] WARNING: no name column found on line 140 +[12:13:07] WARNING: no name column found on line 141 +[12:13:07] WARNING: no name column found on line 142 +[12:13:07] WARNING: no name column found on line 143 +[12:13:07] WARNING: no name column found on line 144 +[12:13:07] WARNING: no name column found on line 145 +[12:13:07] WARNING: no name column found on line 146 +[12:13:07] WARNING: no name column found on line 147 +[12:13:07] WARNING: no name column found on line 148 +[12:13:07] WARNING: no name column found on line 149 +[12:13:07] WARNING: no name column found on line 150 +[12:13:07] WARNING: no name column found on line 151 +[12:13:07] WARNING: no name column found on line 152 +[12:13:07] WARNING: no name column found on line 153 +[12:13:07] WARNING: no name column found on line 154 +[12:13:07] WARNING: no name column found on line 155 +[12:13:07] WARNING: no name column found on line 156 +[12:13:07] WARNING: no name column found on line 157 +[12:13:07] WARNING: no name column found on line 158 +[12:13:07] WARNING: no name column found on line 159 +[12:13:07] WARNING: no name column found on line 160 +[12:13:07] WARNING: no name 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...... ---------------------------------------------------------------------- -Ran 10 tests in 0.152s +Ran 10 tests in 0.182s OK .................. ---------------------------------------------------------------------- -Ran 18 tests in 0.946s +Ran 18 tests in 1.210s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.103s +Ran 3 tests in 0.121s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.039s +Ran 8 tests in 0.053s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.029s +Ran 2 tests in 0.030s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.018s +Ran 2 tests in 0.022s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.082s +Ran 1 test in 0.100s OK ........ @@ -32501,28 +32533,28 @@ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- -Ran 4 tests in 0.006s +Ran 4 tests in 0.009s FAILED (errors=1) !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.020s +Ran 7 tests in 0.019s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.024s +Ran 4 tests in 0.025s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 3.499s +Ran 4 tests in 3.847s OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.067s +Ran 10 tests in 0.069s OK . @@ -32532,7 +32564,7 @@ OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.005s +Ran 10 tests in 0.006s OK ....E @@ -32551,15 +32583,15 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 5 tests in 0.081s +Ran 5 tests in 0.065s FAILED (errors=1) !!! TEST FAILURE: python UnitTestGobbi.py {} -................[03:06:51] Molecule does not have explicit Hs. Consider calling AddHs() -[03:06:51] Molecule does not have explicit Hs. Consider calling AddHs() +................[12:13:33] Molecule does not have explicit Hs. Consider calling AddHs() +[12:13:33] Molecule does not have explicit Hs. Consider calling AddHs() ..... ---------------------------------------------------------------------- -Ran 21 tests in 8.790s +Ran 21 tests in 10.088s OK mol_197 @@ -32573,7 +32605,7 @@ Ran 1 test in 0.000s OK -...[03:06:52] +...[12:13:33] **** Pre-condition Violation @@ -32584,65 +32616,65 @@ . ---------------------------------------------------------------------- -Ran 4 tests in 0.030s +Ran 4 tests in 0.032s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 8.316s +Ran 2 tests in 9.591s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.103s +Ran 2 tests in 0.153s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.014s +Ran 3 tests in 0.018s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.022s +Ran 4 tests in 0.037s OK -.....[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors -[03:07:03] WARNING: not removing hydrogen atom without neighbors +.....[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors +[12:13:46] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- -Ran 10 tests in 0.372s +Ran 10 tests in 0.499s OK -ssssss[03:07:04] No suitable metadata found. -.[03:07:04] No suitable metadata found. +ssssss[12:13:48] No suitable metadata found. +.[12:13:48] No suitable metadata found. ......s/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually warnings.warn( ..... ---------------------------------------------------------------------- -Ran 19 tests in 0.452s +Ran 19 tests in 0.700s OK (skipped=7) sss. ---------------------------------------------------------------------- -Ran 4 tests in 0.942s +Ran 4 tests in 1.138s OK (skipped=3) sss @@ -32652,33 +32684,33 @@ OK (skipped=3) .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.579s +Ran 10 tests in 0.959s OK -..[03:07:07] SMARTS Parse Error: syntax error while parsing: boromicacid -[03:07:07] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -[03:07:07] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -[03:07:07] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -[03:07:07] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -[03:07:07] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -[03:07:07] reaction has no reactants -[03:07:07] reaction has no products -[03:07:07] initialization failed -[03:07:07] reaction has no reactants -[03:07:07] reaction has no products +..[12:13:53] SMARTS Parse Error: syntax error while parsing: boromicacid +[12:13:53] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +[12:13:53] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +[12:13:53] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +[12:13:53] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +[12:13:53] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +[12:13:53] reaction has no reactants +[12:13:53] reaction has no products +[12:13:53] initialization failed +[12:13:53] reaction has no reactants +[12:13:53] reaction has no products . ---------------------------------------------------------------------- -Ran 3 tests in 0.030s +Ran 3 tests in 0.042s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.013s +Ran 4 tests in 0.015s OK .................... ---------------------------------------------------------------------- -Ran 20 tests in 0.103s +Ran 20 tests in 0.134s OK !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} @@ -32688,10 +32720,14 @@ !!! TEST FAILURE: python test_list.py {'dir': 'FeatMaps'} !!! TEST FAILURE: python test_list.py {'dir': 'Pharm2D'} +5: [12:15:26] Finished: testMultipleTimes() +5: [12:15:26] +5: ----------------------------------------- +208/208 Test #5: testConcurrentQueue .................... Passed 311.01 sec 98% tests passed, 5 tests failed out of 208 -Total Test time (real) = 178.47 sec +Total Test time (real) = 311.31 sec The following tests FAILED: 22 - pyAlignment (Failed) @@ -32702,7 +32738,7 @@ Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu' -dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15 returned exit code 2 +dh_auto_test: error: cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 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 @@ -32712,7 +32748,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202209.3' dh_auto_install - cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/reproducible-path/rdkit-202209.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202209.3 -B/build/reproducible-path/rdkit-202209.3/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -35374,32 +35410,32 @@ dh_shlibdeps -a -O--buildsystem=cmake -O--parallel 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 rdkit-doc: 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: 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: 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-data: substitution variable ${shlibs:Depends} 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 rdkit-data: 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: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-doc: 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: package librdkit-dev: substitution variable ${python3:Depends} unused, but is 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: 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 dh_md5sums -O--buildsystem=cmake -O--parallel dh_builddeb -O--buildsystem=cmake -O--parallel dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202209.3-1_amd64.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202209.3-1_amd64.deb'. dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202209.3-1_all.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202209.3-1_all.deb'. -dpkg-deb: building package 'librdkit1' in '../librdkit1_202209.3-1_amd64.deb'. +dpkg-deb: building package 'librdkit1-dbgsym' in '../librdkit1-dbgsym_202209.3-1_amd64.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202209.3-1_amd64.deb'. +dpkg-deb: building package 'librdkit1' in '../librdkit1_202209.3-1_amd64.deb'. dpkg-deb: building package 'postgresql-15-rdkit' in '../postgresql-15-rdkit_202209.3-1_amd64.deb'. -dpkg-deb: building package 'librdkit1-dbgsym' in '../librdkit1-dbgsym_202209.3-1_amd64.deb'. dpkg-deb: building package 'postgresql-15-rdkit-dbgsym' in '../postgresql-15-rdkit-dbgsym_202209.3-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202209.3-1_amd64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202209.3-1_amd64.changes @@ -35408,12 +35444,14 @@ 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/1744204/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1744204/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/1227684 and its subdirectories -I: Current time: Thu Jan 11 03:10:58 -12 2024 -I: pbuilder-time-stamp: 1704985858 +I: removing directory /srv/workspace/pbuilder/1744204 and its subdirectories +I: Current time: Thu Feb 13 12:18:57 +14 2025 +I: pbuilder-time-stamp: 1739398737