Diff of the two buildlogs: -- --- b1/build.log 2023-04-18 08:43:21.165256705 +0000 +++ b2/build.log 2023-04-18 10:56:39.138448333 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 17 16:30:26 -12 2023 -I: pbuilder-time-stamp: 1681792226 +I: Current time: Tue May 21 05:07:54 +14 2024 +I: pbuilder-time-stamp: 1716217674 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./rdkit_202209.3.orig.tar.xz] I: copying [./rdkit_202209.3-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Jan 14 00:24:43 2023 -12 +gpgv: Signature made Sun Jan 15 02:24:43 2023 +14 gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./rdkit_202209.3-1.dsc: no acceptable signature found @@ -33,52 +33,84 @@ 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/12876/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/14287/tmp/hooks/D01_modify_environment starting +debug: Running on codethink11-arm64. +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 May 21 05:08 /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/14287/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/14287/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='12876' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=14287 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.WRYpBM1Q/pbuilderrc_HDcP --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.WRYpBM1Q/b1 --logfile b1/build.log rdkit_202209.3-1.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.WRYpBM1Q/pbuilderrc_K0d0 --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.WRYpBM1Q/b2 --logfile b2/build.log --extrapackages usrmerge rdkit_202209.3-1.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink14-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 15 22:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/12876/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 19 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/14287/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -518,7 +550,7 @@ Get: 329 http://deb.debian.org/debian bookworm/main arm64 texlive-latex-recommended all 2022.20230122-3 [8880 kB] Get: 330 http://deb.debian.org/debian bookworm/main arm64 texlive-pictures all 2022.20230122-3 [15.8 MB] Get: 331 http://deb.debian.org/debian bookworm/main arm64 texlive-latex-extra all 2022.20230122-3 [19.2 MB] -Fetched 358 MB in 9s (40.7 MB/s) +Fetched 358 MB in 8s (44.1 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 ... 19616 files and directories currently installed.) @@ -1921,8 +1953,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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/14287/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/14287/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/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 @@ -2071,21 +2112,21 @@ make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend +make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/External/catch /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/catch /build/rdkit-202209.3/obj-aarch64-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 make[4]: Entering directory 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'/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/External/RingFamilies /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/RingFamilies /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/DependInfo.cmake --color= -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/External/GA /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/GA /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/GA/CMakeFiles/ga.dir/DependInfo.cmake --color= make -f 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-I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkitCatch.dir/catch_main.cpp.o -MF CMakeFiles/rdkitCatch.dir/catch_main.cpp.o.d -o CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -c /build/rdkit-202209.3/Code/RDGeneral/catch_main.cpp make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ML/Cluster/Murtagh /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/rdkit-202209.3/Code/RDGeneral/RDGeneralExceptions.cpp make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 0%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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 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-I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o -MF CMakeFiles/RDStreams.dir/streams.cpp.o.d -o CMakeFiles/RDStreams.dir/streams.cpp.o -c /build/rdkit-202209.3/Code/RDStreams/streams.cpp -[ 2%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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 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-DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_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 -Dhc_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -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/hcdriver.c.o -MF CMakeFiles/hc.dir/hcdriver.c.o.d -o CMakeFiles/hc.dir/hcdriver.c.o -c /build/rdkit-202209.3/Code/ML/Cluster/Murtagh/hcdriver.c [ 3%] Linking C shared library ../../../../lib/libRDKithc.so @@ -2160,18 +2201,18 @@ cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2022.09.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 3%] Built target hc +[ 3%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/Chromosome.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/ga/Chromosome.cpp.o -MF CMakeFiles/ga.dir/ga/Chromosome.cpp.o.d -o CMakeFiles/ga.dir/ga/Chromosome.cpp.o -c /build/rdkit-202209.3/External/GA/ga/Chromosome.cpp +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/RDGeneral/RDLog.cpp +[ 3%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/ga/IntegerStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o -c /build/rdkit-202209.3/External/GA/ga/IntegerStringChromosomePolicy.cpp [ 4%] Building CXX object External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/ga/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/rdkit-202209.3/External/GA/ga/BinaryStringChromosomePolicy.cpp [ 4%] Building CXX object External/GA/CMakeFiles/ga.dir/util/RandomUtil.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/RandomUtil.cpp.o -MF CMakeFiles/ga.dir/util/RandomUtil.cpp.o.d -o CMakeFiles/ga.dir/util/RandomUtil.cpp.o -c /build/rdkit-202209.3/External/GA/util/RandomUtil.cpp [ 4%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/External/GA/util/Util.cpp -[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/RDGeneral/utils.cpp -[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/rdkit-202209.3/Code/RDGeneral/RDGeneralExceptions.cpp -[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/RDGeneral/RDLog.cpp [ 5%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -MF CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o.d -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /build/rdkit-202209.3/Code/RDGeneral/LocaleSwitcher.cpp [ 5%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o @@ -2179,12 +2220,12 @@ [ 5%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2022.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2022.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 5%] Built target ga [ 5%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2022.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2022.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 5%] Built target ga cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2022.09.3 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 5%] Built target RDStreams @@ -2195,61 +2236,61 @@ make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 5%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= +make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Numerics/EigenSolvers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= -make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/RDBoost /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDBoost /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= -make -f 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-I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/rdkit-202209.3/Code/DataStructs/BitVect.cpp cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 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CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/rdkit-202209.3/Code/RDGeneral/testDict.cpp [ 5%] Linking CXX executable testConcurrentQueue cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -2296,31 +2337,27 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Catalogs/CatalogEntry.cpp -[ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/obj-aarch64-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%] Linking CXX executable testMatrices +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -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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make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/rdkit-202209.3/Code/DataStructs/ExplicitBitVect.cpp +[ 6%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Catalogs/CatalogEntry.cpp +[ 6%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 6%] Built target RDBoost -make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend +[ 6%] Built target Catalogs +make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/RDBoost/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDBoost/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ML/Cluster/Murtagh /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make 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-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 +[ 7%] Linking CXX executable testDict +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 7%] Built target testQuery +[ 7%] Built target testDict +[ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.cpp [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/DiscreteDistMat.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, @@ -2390,6 +2431,23 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/smart_ptr.hpp:19, + from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/rdkit-202209.3/Code/ML/Cluster/Murtagh/Clustering.cpp:12: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, @@ -2401,29 +2459,17 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/DiscreteValueVect.cpp [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/FPBReader.cpp [ 7%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/MultiFPBReader.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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/ML/Cluster/Murtagh/Clustering.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp +[ 7%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 7%] Built target Clustering [ 8%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 @@ -2438,16 +2484,6 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 8%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/SimDivPickers/testPickers.cpp -[ 8%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 8%] Built target Clustering -[ 8%] Linking CXX executable testSimDivPickers -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2022.09.3 ../../lib/libRDKithc.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 8%] Built target testSimDivPickers [ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 @@ -2458,49 +2494,54 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Geometry /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend +make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DataStructs/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/Wrap /build/rdkit-202209.3/obj-aarch64-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 -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/rdkit-202209.3/Code/DataStructs/testDatastructs.cpp -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -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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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/rdkit-202209.3/Code/DataStructs/testFPB.cpp [ 8%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs && /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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/DataStructs/testMultiFPB.cpp -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build +[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs && /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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c 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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/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/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.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, @@ -2516,10 +2557,12 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:12: + from /build/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp:13: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/Transform2D.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2534,34 +2577,35 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/DataStructs/Wrap/DataStructs.cpp:13: + from /build/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.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( | ^~~~~~~~~~~~~~~~~~~~ -[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/Transform2D.cpp [ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp -[ 10%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/rdkit-202209.3/Code/Geometry/Transform3D.cpp +[ 9%] Linking CXX executable testFPB +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 10%] Built target rdMetricMatrixCalc +[ 9%] Built target testFPB make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/SimDivPickers/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o +[ 10%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp -[ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/rdkit-202209.3/Code/Geometry/Transform3D.cpp -[ 11%] Linking CXX executable testFPB -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 +[ 10%] Linking CXX executable testMultiFPB +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 11%] Built target testFPB +[ 11%] Built target testMultiFPB make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ML/InfoTheory /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= @@ -2570,15 +2614,28 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 11%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/InfoTheory/InfoBitRanker.cpp -[ 11%] Linking CXX executable testMultiFPB -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 static library librdkitCatch.a -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -/usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -[ 11%] Built target testMultiFPB +[ 11%] Built target rdMetricMatrixCalc +[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/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, + 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/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/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( + | ^~~~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/UniformGrid3D.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, @@ -2595,10 +2652,14 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp:11: + from /build/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%] Linking CXX static library librdkitCatch.a +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' [ 11%] Built target rdkitCatch @@ -2624,12 +2685,12 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:12: + from /build/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/GridUtils.cpp +[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp [ 11%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 @@ -2644,8 +2705,13 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 11%] Building CXX object Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/RDGeneral/catch_logs.cpp -[ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp +[ 11%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/GridUtils.cpp +[ 11%] Linking CXX executable testDataStructs +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 11%] Built target testDataStructs make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/SimDivPickers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/DependInfo.cmake --color= @@ -2654,38 +2720,8 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 11%] Building CXX object Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/catch_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/SimDivPickers/catch_tests.cpp -[ 11%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 11%] Built target RDGeometryLib -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ML/InfoTheory/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp -[ 12%] Linking CXX executable testDataStructs -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Built target testDataStructs -make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ML/Data /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Data /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/Data/cQuantize.cpp -[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +[ 11%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp -[ 12%] Linking CXX executable dictTestsCatch -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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, @@ -2693,32 +2729,48 @@ 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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/DataStructs/Wrap/SparseIntVect.cpp:11: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Linking CXX executable logTestsCatch +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 11%] Linking CXX executable logTestsCatch cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 -[ 12%] Built target dictTestsCatch -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 11%] Linking CXX executable dictTestsCatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 11%] Built target logTestsCatch +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend +[ 11%] Built target dictTestsCatch make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= +make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ML/InfoTheory/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ML/Data /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Data /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 11%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/Data/cQuantize.cpp +[ 12%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp +[ 12%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Built target logTestsCatch +[ 12%] Built target RDGeometryLib make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= @@ -2727,19 +2779,6 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Atom.cpp -[ 12%] Linking CXX executable pickersTestsCatch -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Built target pickersTestsCatch -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Numerics/Alignment /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Numerics/Alignment/AlignPoints.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2754,7 +2793,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp:12: + from /build/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2772,13 +2811,25 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp:12: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 12%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 +[ 12%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp +[ 12%] Linking CXX executable pickersTestsCatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 12%] Built target pickersTestsCatch +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Numerics/Alignment /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 12%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Numerics/Alignment/AlignPoints.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2796,36 +2847,59 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -cd /build/rdkit-202209.3/obj-aarch64-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 +[ 12%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Built target ChemicalFeatures +[ 12%] Built target cQuantize make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Geometry /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 12%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 [ 12%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/rdkit-202209.3/Code/Geometry/testTransforms.cpp -[ 12%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/obj-aarch64-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 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 12%] Built target Alignment +[ 12%] Built target rdBase make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Geometry /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= -[ 12%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so [ 13%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/Geometry/testGrid.cpp +[ 13%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp +[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + 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/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 13%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 13%] Built target cQuantize +[ 13%] Built target Alignment make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Geometry /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake --color= @@ -2834,31 +2908,8 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 13%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/Geometry/catch_tests.cpp -[ 13%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp -[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp -[ 13%] Linking CXX shared module ../../../rdkit/rdBase.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so -[ 14%] Linking CXX executable testTransforms -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 14%] Built target rdBase -make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Geometry/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 14%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 14%] Built target testTransforms -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Numerics /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/QueryAtom.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, @@ -2877,21 +2928,57 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +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/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/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( + | ^~~~~~~~~~~~~~~~~~~~ +[ 13%] Linking CXX executable testGrid +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 13%] Built target testGrid +make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Geometry/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 13%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp +[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp +[ 14%] Linking CXX executable testTransforms +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 14%] Built target testTransforms +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Numerics /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 14%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics && /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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/rdkit-202209.3/Code/Numerics/testConrec.cpp -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/QueryAtom.cpp -[ 14%] Linking CXX executable testGrid -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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%] Linking CXX executable geometryTestsCatch cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 14%] Built target testGrid +[ 14%] Built target geometryTestsCatch make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/Numerics/Alignment /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= @@ -2900,10 +2987,12 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 14%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/Numerics/Alignment/testAlignment.cpp -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 14%] Built target geometryTestsCatch -[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/QueryBond.cpp +[ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp +[ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp +[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -2918,7 +3007,7 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp:13: + from /build/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ @@ -2936,17 +3025,13 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/Geometry/Wrap/Point.cpp:11: + from /build/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 14%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp [ 14%] Linking CXX executable testConrec cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 -[ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 14%] Built target testConrec make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend @@ -2957,21 +3042,8 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 14%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp -[ 15%] Linking CXX executable testAlignment -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 15%] Built target testAlignment -make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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 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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Bond.cpp +[ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -2982,7 +3054,7 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -2996,109 +3068,36 @@ 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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -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/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp:12: + from /build/rdkit-202209.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolOps.cpp -[ 15%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 15%] Linking CXX executable testAlignment +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 15%] Built target rdInfoTheory -[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FindRings.cpp +[ 15%] Built target testAlignment +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 15%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp [ 15%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 15%] Built target rdSimDivPickers -[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp -[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp -[ 15%] Linking CXX executable testChemicalFeatures -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 15%] Built target testChemicalFeatures -[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp -[ 15%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 15%] Built target rdAlignment -[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ROMol.cpp -[ 16%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp -/build/rdkit-202209.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': -/build/rdkit-202209.3/Code/GraphMol/FindRings.cpp:1350:36: warning: unused parameter 'mol' [-Wunused-parameter] - 1350 | void findRingFamilies(const ROMol &mol) { - | ~~~~~~~~~~~~~^~~ -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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/DataStructs/Wrap/wrap_BitOps.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp:11: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Bond.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3109,13 +3108,16 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp:10: + from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-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, @@ -3123,16 +3125,61 @@ 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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/DataStructs/Wrap/wrap_FPB.cpp:10: + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/rdkit-202209.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 15%] Built target rdInfoTheory +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolOps.cpp +[ 15%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/ChemicalFeatures/testChemicalFeatures.cpp +[ 15%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 15%] Built target rdAlignment +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FindRings.cpp +[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/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/rdkit-202209.3/Code/Geometry/Wrap/UniformGrid3D.cpp +[ 16%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp +[ 16%] Linking CXX executable testChemicalFeatures +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 16%] Built target testChemicalFeatures +[ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp +/build/rdkit-202209.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': +/build/rdkit-202209.3/Code/GraphMol/FindRings.cpp:1350:36: warning: unused parameter 'mol' [-Wunused-parameter] + 1350 | void findRingFamilies(const ROMol &mol) { + | ~~~~~~~~~~~~~^~~ 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, @@ -3151,16 +3198,8 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp -[ 16%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/RWMol.cpp [ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/PeriodicTable.cpp -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -3171,7 +3210,7 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/DataStructs/Wrap/wrap_Utils.cpp:11: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ @@ -3188,15 +3227,15 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/Geometry/Wrap/rdGeometry.cpp:11: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ /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/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/QueryOps.cpp +[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/atomic_data.cpp In file included from /usr/include/c++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, @@ -3207,28 +3246,32 @@ /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolPickler.cpp -[ 16%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/QueryOps.cpp +[ 17%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 16%] Built target rdGeometry -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +[ 17%] Built target cDataStructs +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolPickler.cpp +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Canon.cpp -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o +[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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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/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/BondIterators.cpp -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Aromaticity.cpp -[ 18%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 18%] Built target cDataStructs +[ 18%] Built target rdGeometry +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Aromaticity.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Kekulize.cpp +[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ConjugHybrid.cpp /build/rdkit-202209.3/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': /build/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:71:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 71 | if (res < 0) { @@ -3243,8 +3286,6 @@ /build/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/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:856:33: required from here /build/rdkit-202209.3/Code/GraphMol/MolPickler.cpp:1666:22: warning: comparison is always false due to limited range of data type [-Wtype-limits] -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ConjugHybrid.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/AddHs.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o @@ -3263,8 +3304,6 @@ cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Resonance.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/StereoGroup.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/new_canon.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, @@ -3280,6 +3319,8 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/new_canon.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SubstanceGroup.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o @@ -3295,68 +3336,68 @@ make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 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[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolTransforms /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/SmilesParse /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/GenericGroups /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups /build/rdkit-202209.3/obj-aarch64-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 -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make 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/build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/PartialCharges /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolCatalog /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/CIPLabeler /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.cpp [ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.cpp cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_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 -DTrajectory_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Trajectory/Trajectory.cpp -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/SmilesParse/SmilesParse.cpp +[ 21%] Building CXX object 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Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/GenericGroups/GenericGroups.cpp [ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp +[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o +[ 21%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/build/rdkit-202209.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Subgraphs/Subgraphs.cpp cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp [ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp @@ -3424,11 +3465,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 23%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Trajectory.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp cd /build/rdkit-202209.3/obj-aarch64-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 make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 23%] Built target MolTransforms @@ -3610,6 +3651,8 @@ cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp [ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/Numerics/Optimizer/LinearSearch.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.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, @@ -3628,8 +3671,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp [ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SLNParse/sln.tab.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, @@ -3724,20 +3765,10 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 25%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/Numerics/Optimizer/testOptimizer.cpp +[ 25%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp [ 25%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/rdkit-202209.3/obj-aarch64-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 -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 25%] Built target SubstructMatch -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ForceField /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/ForceField.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, @@ -3753,15 +3784,25 @@ /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/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp /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/lex.yysln.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SLNParse/lex.yysln.cpp +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/rdkit-202209.3/obj-aarch64-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 +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 25%] Built target SubstructMatch +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ForceField /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 25%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/ForceField.cpp [ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SLNParse/lex.yysln.cpp [ 25%] Linking CXX executable testOptimizer cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -3794,6 +3835,13 @@ | ^~~~~~~~~~ [ 26%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/rdkit-202209.3/Code/ForceField/UFF/AngleBend.cpp +[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 26%] Built target rdMolTransforms +[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SmilesParse/smarts.tab.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -3812,13 +3860,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 26%] Built target rdMolTransforms -[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 26%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -3833,35 +3874,37 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 26%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp [ 26%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 26%] Built target rdMolCatalog -[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ 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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/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/rdkit-202209.3/Code/ForceField/UFF/BondStretch.cpp -[ 26%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 27%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /build/rdkit-202209.3/obj-aarch64-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 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/BondStretch.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.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, @@ -3880,15 +3923,15 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp [ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 27%] Built target rdMolInterchange -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.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, @@ -3907,68 +3950,83 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 27%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/Inversion.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 27%] Built target rdSLNParse +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/Nonbonded.cpp [ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK 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Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp -[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o +[ 28%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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 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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp +[ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 29%] Built target rdSLNParse +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/TorsionAngle.cpp -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/DistanceConstraint.cpp [ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 29%] Built target rdShapeHelpers -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.cpp -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/TorsionConstraint.cpp -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/Params.cpp -[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/MMFF/AngleBend.cpp -[ 30%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/DistanceConstraint.cpp +[ 29%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/AngleConstraint.cpp cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 30%] Built target CIPLabeler +[ 29%] Built target CIPLabeler make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 30%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o +[ 29%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/TorsionConstraint.cpp +[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/PositionConstraint.cpp +[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/UFF/Params.cpp +[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/MMFF/AngleBend.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/rdkit-202209.3/Code/ForceField/MMFF/BondStretch.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.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/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/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("") + | ^~~~~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/rdkit-202209.3/Code/ForceField/MMFF/OopBend.cpp [ 30%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so @@ -3987,39 +4045,16 @@ cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolAlign_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/rdkit-202209.3/Code/ForceField/MMFF/TorsionAngle.cpp -/build/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': -/build/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 27 | const MMFFStbn *mmffStbnParams) { - | ^ [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/MMFF/Nonbonded.cpp [ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/MMFF/DistanceConstraint.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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/MMFF/AngleConstraint.cpp -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/rdkit-202209.3/Code/ForceField/MMFF/TorsionConstraint.cpp -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/rdkit-202209.3/Code/ForceField/MMFF/PositionConstraint.cpp -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp +/build/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': +/build/rdkit-202209.3/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 27 | const MMFFStbn *mmffStbnParams) { + | ^ [ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -4033,7 +4068,13 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 31%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/rdkit-202209.3/Code/ForceField/MMFF/TorsionConstraint.cpp +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/rdkit-202209.3/Code/ForceField/MMFF/PositionConstraint.cpp +[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o [ 32%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/MMFF/Params.cpp cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' @@ -4081,9 +4122,6 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/test-valgrind.cpp -[ 33%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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 [ 33%] Linking CXX executable graphmolcpTest cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -4097,6 +4135,9 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/catch_moliterators.cpp +[ 33%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Built target ForceField @@ -4134,11 +4175,13 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/Fingerprints.cpp -[ 33%] Linking CXX executable test-valgrind -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 33%] Linking CXX executable smiTest2 +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 33%] Built target test-valgrind +[ 33%] Built target smiTest2 make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FilterCatalog /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= @@ -4147,14 +4190,14 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FilterCatalog/Filters.cpp -[ 33%] Linking CXX executable smiTest2 -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl [ 33%] Linking CXX executable moliteratorTestsCatch cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 33%] Linking CXX executable test-valgrind +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 33%] Built target smiTest2 +[ 33%] Built target test-valgrind make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Subgraphs /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake --color= @@ -4173,11 +4216,12 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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 -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/Subgraphs/test2.cpp -[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp [ 33%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 33%] Linking CXX executable graphmolqueryTest +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Built target ChemTransforms @@ -4189,9 +4233,6 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -[ 33%] Linking CXX executable graphmolqueryTest -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Built target graphmolqueryTest make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend @@ -4202,10 +4243,12 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 33%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges && /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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/PartialCharges/test1.cpp -[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp +[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp +[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 33%] Linking CXX executable testSubgraphs2 cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubgraphs2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubgraphs2.dir/test2.cpp.o -o testSubgraphs2 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -4247,12 +4290,12 @@ cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_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 -DReducedGraphs_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp [ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp -[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp [ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp -[ 35%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.cpp +[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.cpp [ 35%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitReducedGraphs.so.1 -o ../../../lib/libRDKitReducedGraphs.so.1.2022.09.3 CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -4267,9 +4310,13 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 35%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/SLNParse/test.cpp +[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp [ 35%] Linking CXX executable smaTest1 cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 35%] Built target smaTest1 make -f Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/depend @@ -4280,14 +4327,14 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 35%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/rdchem.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/rdchem.cpp -[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp -[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp -[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp -[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o +[ 35%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPMol.cpp +[ 35%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.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, @@ -4305,30 +4352,24 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 36%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp -[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp [ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp [ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FragCatalog/FragCatParams.cpp -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Fingerprints/MACCS.cpp -[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/MHFP.cpp -[ 36%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/aarch64-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/rdkit-202209.3/obj-aarch64-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 +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp +[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 36%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 36%] Built target FilterCatalog +[ 36%] Built target MolChemicalFeatures make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Abbreviations /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake --color= @@ -4337,12 +4378,23 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 36%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Abbreviations/Abbreviations.cpp -[ 36%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/rdkit-202209.3/obj-aarch64-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 +[ 36%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp +[ 36%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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 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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Table.cpp +[ 36%] Linking CXX executable testSLNParse +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 36%] Built target MolChemicalFeatures +[ 36%] Built target testSLNParse make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Depictor /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= @@ -4351,28 +4403,19 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 37%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd 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CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Depictor/RDDepictor.cpp -[ 37%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp -[ 38%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp -[ 38%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Table.cpp -[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK 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/build/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp -[ 39%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp -[ 39%] Linking CXX executable testSLNParse -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 38%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 39%] Built target testSLNParse +[ 38%] Built target FragCatalog make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/External/CoordGen/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/CoordGen/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 39%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o +[ 38%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/CoordGen/Wrap && /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 -DrdCoordGen_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/rdkit-202209.3/External/CoordGen/Wrap/rdCoordGen.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, @@ -4392,26 +4435,14 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 40%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 40%] Built target FragCatalog -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake --color= -[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Edge.cpp -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Node.cpp [ 40%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp -[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Edge.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, @@ -4430,34 +4461,46 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/Sort.cpp +[ 40%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl [ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -[ 40%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp -[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp -[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 40%] Built target Fingerprints +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers /build/rdkit-202209.3/obj-aarch64-linux-gnu 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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/rdkit-202209.3/Code/GraphMol/Wrap/Atom.cpp -[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp +[ 40%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp [ 40%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake 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/build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2022.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so -[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 40%] Built target Abbreviations -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -4476,6 +4519,12 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp +[ 40%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.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, @@ -4483,42 +4532,44 @@ 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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.h:36, - from /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp:32: + 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/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 40%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 40%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/aarch64-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 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 40%] Built target rdCoordGen -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 40%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp -[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp -[ 41%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp -[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp -[ 41%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp +[ 40%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 40%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp +[ 41%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/aarch64-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/rdkit-202209.3/obj-aarch64-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 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, @@ -4526,16 +4577,39 @@ 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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.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/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( | ^~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 41%] Built target FilterCatalog +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake --color= /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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 41%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/Rule4b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/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, @@ -4543,41 +4617,58 @@ 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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp +[ 41%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Depictor/DepictUtils.cpp [ 41%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 41%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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 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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 42%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp -[ 42%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-Drdchem_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp +/build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': +/build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:419:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); + | ^ +[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 42%] Linking CXX executable testCIPLabeler +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ReducedGraphs/test1.cpp +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 42%] Built target testCIPLabeler +make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 43%] Building CXX object Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ReducedGraphs/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 -DrdReducedGraphs_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.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, @@ -4596,36 +4687,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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-ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Bond.cpp -[ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp -[ 43%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 43%] Linking CXX shared library ../../../lib/libRDKitDepictor.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so 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-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/rdkit-202209.3/Code/GraphMol/ReducedGraphs/Wrap/rdReducedGraphs.cpp -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 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changed to match C++14 in GCC 10.1 - 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); - | ^ -[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 44%] Linking CXX executable testReducedGraphs -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp +[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 44%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/CDXMLParser.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, @@ -4675,14 +4754,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 44%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -4697,12 +4768,40 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp:12: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 44%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp +[ 44%] Linking CXX executable testReducedGraphs +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 44%] Built target testReducedGraphs +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make 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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 44%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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../../../../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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 44%] Built target rdReducedGraphs +[ 45%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -4717,25 +4816,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp:11: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 44%] Built target rdReducedGraphs -make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 44%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/CDXMLParser.cpp -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/Rule6.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, @@ -4750,31 +4834,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp:11: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp -[ 45%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 45%] 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/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Depictor/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 45%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp -[ 46%] Linking CXX executable testCIPLabeler -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.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, @@ -4782,29 +4845,17 @@ 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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:12: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.h:36, + from /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp:32: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 46%] Built target testCIPLabeler -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 46%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp -[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Conformer.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, @@ -4819,23 +4870,43 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp:11: + from /build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 46%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +[ 46%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 46%] Built target ForceFieldHelpers +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DistGeom /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 46%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong 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-I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp +[ 46%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Conformer.cpp [ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat 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'/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 47%] Built target rdAbbreviations -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake --color= +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ForceField/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 47%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +[ 48%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/Wrap/ForceField.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, @@ -4849,26 +4920,13 @@ 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/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:13: + from /build/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 47%] Built target rdMolChemicalFeatures -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.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, @@ -4887,6 +4945,17 @@ /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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 48%] Built target rdDepictor +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 48%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -4900,13 +4969,11 @@ 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/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: + from /build/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/rdkit-202209.3/Code/GraphMol/Wrap/Mol.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ In 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, @@ -4921,60 +4988,25 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:11: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 47%] Built target rdDepictor +[ 48%] Built target rdMolChemicalFeatures make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolAlign /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 47%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +[ 48%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp -[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +[ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DistGeom /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 47%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ 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/build/rdkit-202209.3/Code/DistGeom/DistGeomUtils.cpp -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp -[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp -[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 48%] Built target rdFingerprintGenerator -[ 49%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.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, @@ -4989,10 +5021,56 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/ForceField/Wrap/ForceField.cpp:12: + from /build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:11: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DistGeom/DistViolationContrib.cpp +[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DistGeom/ChiralViolationContrib.cpp +[ 48%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/RingInfo.cpp +[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileParser.cpp +[ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 49%] Built target rdForceFieldHelpers +[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd 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CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp +[ 49%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 +[ 49%] Built target O3AAlign +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 49%] Built target DistGeometry +make -f 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Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5011,17 +5089,14 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileParser.cpp -[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/rdkit-202209.3/obj-aarch64-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 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp -[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/EditableMol.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileWriter.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK 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/build/rdkit-202209.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FileParsers/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, @@ -5040,16 +5115,14 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 50%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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 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../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 50%] Built target O3AAlign -[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp +[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/MonomerInfo.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/SDWriter.cpp +[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/ResonanceMolSupplier.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, @@ -5068,6 +5141,21 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 50%] Built target rdfiltercatalog +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DistGeom /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 50%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom && /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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/DistGeom/testDistGeom.cpp +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK 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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, @@ -5088,8 +5176,27 @@ /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/StereoGroup.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/SmilesWriter.cpp +[ 51%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp +[ 51%] Linking CXX executable testDistGeom +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 51%] Built target testDistGeom +make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DistGeom/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 51%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp +[ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -5097,23 +5204,16 @@ 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/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp:12: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -/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/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DistGeom/DistViolationContrib.cpp -[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -5127,17 +5227,11 @@ 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/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp:12: + from /build/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -/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/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/DistGeom/ChiralViolationContrib.cpp -[ 50%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5151,38 +5245,36 @@ 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/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:12: + from /build/rdkit-202209.3/Code/GraphMol/Wrap/MolBundle.cpp:12: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 50%] Built target rdForceField -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp -[ 50%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so -cd /build/rdkit-202209.3/obj-aarch64-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 +[ 51%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/StereoGroup.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileParser.cpp +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileWriter.cpp +[ 51%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 50%] Built target DistGeometry -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/DistGeomHelpers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake --color= +[ 51%] Built target DistGeom +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF 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../../../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/aarch64-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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp -[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp +[ 52%] Built target DistGeomHelpers +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FileParsers/PDBWriter.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/PDBSupplier.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, @@ -5196,13 +5288,25 @@ 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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp:10: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 50%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FileParsers/CMLWriter.cpp +[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/SubstanceGroup.cpp +[ 53%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/Chirality.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileWriter.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileParser.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -5210,51 +5314,19 @@ 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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, - from /build/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.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/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( | ^~~~~~~~~~~~~~~~~~~~ -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DistGeom /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 50%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom && /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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/DistGeom/testDistGeom.cpp -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/DistGeom/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 50%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MolFileWriter.cpp -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp -[ 50%] Linking CXX executable testDistGeom -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 50%] Built target testDistGeom -[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp -[ 51%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 51%] Built target DistGeomHelpers -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/SDWriter.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, @@ -5269,46 +5341,10 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/DistGeom/Wrap/DistGeom.cpp:12: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 51%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 51%] Built target rdchem -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/SmilesWriter.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp -[ 52%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 52%] Built target DistGeom -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/TDTWriter.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/TplFileParser.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FileParsers/PDBParser.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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 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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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 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-I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileWriter.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileParser.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/ProximityBonds.cpp.o -MF CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o.d -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o @@ -5325,6 +5361,11 @@ cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp +[ 54%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 54%] Built target rdchem [ 54%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -5332,69 +5373,69 @@ make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 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[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/External/CoordGen /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/CoordGen /build/rdkit-202209.3/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake --color= +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ForceField/UFF /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/UFF /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake --color= make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/ForceField/MMFF /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake --color= -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/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake --color= -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-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 +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake --color= -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/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake --color= +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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/rdkit-202209.3/External/CoordGen/test.cpp make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 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make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build -[ 54%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -[ 55%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-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 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/test1.cpp +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code/ForceField/MMFF/testMMFFForceField.cpp +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/molopstest.cpp +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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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/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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/test1.cpp +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/testPickler.cpp +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/testPicklerGlobalSettings.cpp [ 55%] Linking CXX executable graphmoltestPicklerGlobalSetting cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so @@ -5460,24 +5501,24 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/catch_graphmol.cpp -[ 57%] Linking CXX executable resMolSupplierTest -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so -[ 57%] Linking CXX executable molBundleTest +[ 56%] Linking CXX executable molBundleTest cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 57%] Built target resMolSupplierTest +[ 56%] Built target molBundleTest make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o +[ 56%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/catch_sgroups.cpp +[ 57%] Linking CXX executable resMolSupplierTest +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../lib/libRDKitDepictor.so.1.2022.09.3 ../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 57%] Built target molBundleTest +[ 57%] Built target resMolSupplierTest make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake --color= @@ -5671,6 +5712,9 @@ [ 62%] Linking CXX executable chiralityTestsCatch cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 62%] Linking CXX executable graphmolMolOpsTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 62%] Built target chiralityTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend @@ -5681,9 +5725,6 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FileParsers/testMol2ToMol.cpp -[ 62%] Linking CXX executable graphmolMolOpsTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 62%] Built target graphmolMolOpsTest make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend @@ -5694,40 +5735,37 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FileParsers/testSequence.cpp -[ 63%] Linking CXX executable smiTest1 -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 62%] Linking CXX executable testSequence +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 63%] Built target smiTest1 +[ 62%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -[ 63%] Linking CXX executable testTplParser +[ 62%] Linking CXX executable testTplParser cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 63%] Built target testTplParser +[ 62%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 63%] 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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 63%] Linking CXX executable testSequence -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so -[ 63%] Linking CXX executable testMol2ToMol -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 63%] Linking CXX executable smiTest1 +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 63%] Built target testSequence +[ 63%] Built target smiTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake --color= @@ -5736,6 +5774,9 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FileParsers/testPropertyLists.cpp +[ 63%] Linking CXX executable testMol2ToMol +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 63%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend @@ -5746,11 +5787,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp -[ 63%] Linking CXX executable testMolSupplier -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so +[ 63%] Linking CXX executable smiTestCatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 63%] Built target testMolSupplier +[ 63%] Built target smiTestCatch make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake --color= @@ -5759,11 +5800,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp -[ 63%] Linking CXX executable smiTestCatch -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 63%] Linking CXX executable testMolSupplier +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 63%] Built target smiTestCatch +[ 63%] Built target testMolSupplier make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Substruct /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake --color= @@ -5785,11 +5826,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Substruct/catch_tests.cpp -[ 64%] Linking CXX executable XYZFileParserCatchTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 64%] Linking CXX executable testMolWriter +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 64%] Built target XYZFileParserCatchTest +[ 64%] Built target testMolWriter make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/GenericGroups /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake --color= @@ -5798,11 +5839,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/GenericGroups/generic_tests.cpp -[ 64%] Linking CXX executable testMolWriter -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 64%] Linking CXX executable XYZFileParserCatchTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 64%] Built target testMolWriter +[ 64%] Built target XYZFileParserCatchTest make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/DependInfo.cmake --color= @@ -5811,11 +5852,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/Crippen.cpp -[ 64%] Linking CXX executable testPropertyLists -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 64%] Linking CXX executable substructTestCatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 64%] Built target testPropertyLists +[ 64%] Built target substructTestCatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake --color= @@ -5824,11 +5865,14 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -[ 64%] Linking CXX executable substructTestCatch -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 64%] Linking CXX executable cdxmlParserCatchTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 64%] Linking CXX executable testPropertyLists make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 64%] Built target substructTestCatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 64%] Built target cdxmlParserCatchTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ChemTransforms /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake --color= @@ -5837,11 +5881,8 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/ChemTransforms/catch_tests.cpp -[ 64%] Linking CXX executable cdxmlParserCatchTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 64%] Built target cdxmlParserCatchTest +[ 64%] Built target testPropertyLists make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FilterCatalog /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake --color= @@ -5865,11 +5906,11 @@ cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FragCatalog/test1.cpp [ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/BCUT.cpp -[ 66%] Linking CXX executable testSubstructMatch -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 66%] Linking CXX executable testGenericGroups +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 66%] Built target testSubstructMatch +[ 66%] Built target testGenericGroups make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake --color= @@ -5878,11 +5919,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -[ 66%] Linking CXX executable testGenericGroups -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 66%] Linking CXX executable testSubstructMatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 66%] Built target testGenericGroups +[ 66%] Built target testSubstructMatch make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Fingerprints /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/DependInfo.cmake --color= @@ -5913,8 +5954,6 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 66%] Linking CXX executable filterCatalogTest cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so @@ -5928,6 +5967,8 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp +[ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 66%] Linking CXX executable testFragCatalog cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so @@ -5941,10 +5982,6 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp -[ 66%] Linking CXX executable chemTransformsTestCatch -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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, @@ -5963,6 +6000,10 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +[ 66%] Linking CXX executable chemTransformsTestCatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 66%] Built target chemTransformsTestCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' @@ -6087,13 +6128,14 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.cpp +[ 67%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so 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/usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 67%] Built target fpTestCatch +[ 67%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake --color= @@ -6102,17 +6144,16 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 67%] Building CXX object 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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/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp -[ 68%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 68%] Built target testMMFFForceFieldHelpersMultiThread +[ 67%] Built target fpTestCatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/MolSurf.cpp [ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp [ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o @@ -6161,8 +6202,6 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/Lipinski.cpp [ 68%] Linking CXX executable testFingerprints cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so @@ -6176,21 +6215,13 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/Lipinski.cpp +[ 68%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp [ 68%] Linking CXX executable testCrystalForceField cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 68%] 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/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 68%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp -[ 68%] Building 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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/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.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, @@ -6209,6 +6240,16 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 68%] 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/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 68%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/testFeatures.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, @@ -6227,8 +6268,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp [ 68%] Linking CXX executable molAlignCatchTest cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so @@ -6242,11 +6281,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp -[ 68%] Linking CXX executable distGeomHelpersCatch -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 68%] Linking CXX executable testUFFForceFieldHelpers +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 68%] Built target distGeomHelpersCatch +[ 68%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolCatalog /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake --color= @@ -6255,11 +6294,13 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolCatalog/test1.cpp -[ 68%] Linking CXX executable testUFFForceFieldHelpers -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp +[ 68%] Linking CXX executable distGeomHelpersCatch +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 68%] Built target testUFFForceFieldHelpers +[ 68%] Built target distGeomHelpersCatch make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FMCS /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake --color= @@ -6292,8 +6333,6 @@ [ 68%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/MQN.cpp make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 68%] Built target rdDistGeom make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend @@ -6304,11 +6343,13 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/Trajectory/trajectoryTest.cpp -[ 68%] Linking CXX executable testFeatures -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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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 -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/rdkit-202209.3/Code/GraphMol/Descriptors/MQN.cpp +[ 68%] Linking CXX executable testShapeHelpers +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 68%] Built target testFeatures +[ 68%] Built target testShapeHelpers make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolInterchange /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake --color= @@ -6317,11 +6358,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 68%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolInterchange/test1.cpp -[ 68%] Linking CXX executable testShapeHelpers -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 68%] Linking CXX executable testFeatures +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 68%] Built target testShapeHelpers +[ 68%] Built target testFeatures make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolInterchange /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake --color= @@ -6348,16 +6389,6 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeometry.so.1.2022.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-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 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-DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp -[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/Property.cpp -[ 69%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libcoordgen.so 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../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 69%] Built target MMPA make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Abbreviations /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake --color= @@ -6366,39 +6397,22 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -MF CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o.d -o CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Abbreviations/catch_tests.cpp -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/aarch64-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 +[ 69%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libz.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 71%] Built target trajectoryTest +[ 69%] Built target MMPA make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MMPA /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 71%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o +[ 69%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp +[ 69%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -6413,15 +6427,17 @@ from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 71%] Linking CXX executable molInterchangeCatchTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 70%] Linking CXX executable trajectoryTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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 +[ 71%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FMCS/Seed.cpp make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 71%] Built target molInterchangeCatchTest +[ 71%] Built target trajectoryTest make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MMPA/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/DependInfo.cmake --color= @@ -6430,11 +6446,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 71%] Building CXX object Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/rdMMPA.cpp -[ 71%] Linking CXX executable molInterchangeTest1 -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so +[ 71%] Linking CXX executable molInterchangeCatchTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 71%] Built target molInterchangeTest1 +[ 71%] Built target molInterchangeCatchTest [ 71%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, @@ -6457,21 +6473,134 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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-ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp -[ 71%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp [ 71%] Linking CXX executable testMMPA cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 71%] Linking CXX executable molInterchangeTest1 +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so 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-I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR2D.cpp +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 71%] Built target molInterchangeTest1 [ 71%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK 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--verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/PBF.cpp +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF 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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/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/MORSE.cpp +[ 72%] Linking CXX shared library ../../../lib/libRDKitFMCS.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libz.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 72%] Built target FMCS +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FMCS /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp +[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -MF 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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/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/WHIM.cpp +[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/CoulombMat.cpp +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FMCS/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 73%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/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 -DrdFMCS_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FMCS/Test /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 73%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 73%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.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/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 73%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp +In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, + from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, + from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, + from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, + from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, + from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, + from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/rdkit-202209.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:13: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/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, @@ -6490,28 +6619,16 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMMPA.so CMakeFiles/rdMMPA.dir/rdMMPA.cpp.o ../../../../lib/libRDKitMMPA.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 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-I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/PMI.cpp +[ 74%] Linking CXX executable testFMCS +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_serialization.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, @@ -6530,26 +6647,21 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp -[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/AUTOCORR3D.cpp -[ 72%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libz.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 72%] Built target FMCS -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FMCS /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake --color= +[ 74%] Built target testFMCS +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp +[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp +[ 74%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp -[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/RDF.cpp +[ 74%] Built target rdFMCS +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.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, @@ -6568,18 +6680,6 @@ /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%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Descriptors/MORSE.cpp -[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp -[ 72%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/SmilesWriter.cpp -[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/GETAWAY.cpp -[ 73%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/WHIM.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/SDWriter.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, @@ -6598,8 +6698,6 @@ /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%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/CoulombMat.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, @@ -6618,8 +6716,6 @@ /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%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/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, @@ -6638,6 +6734,12 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/TDTWriter.cpp +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -6656,12 +6758,13 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/PDBWriter.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp -[ 74%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o +[ 75%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +[ 75%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.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, @@ -6680,27 +6783,27 @@ /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/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/FMCS/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake --color= +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so +[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -o testFMCS ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_serialization.so +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ChemReactions /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Reaction.cpp +make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/FMCS/Test/testFMCS.cpp +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/test.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, @@ -6737,97 +6840,42 @@ /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/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend +make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake --color= +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp [ 75%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ 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/usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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 ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_serialization.so -make[4]: Leaving 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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/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp -[ 76%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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-I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp +[ 77%] Linking CXX executable testAUTOCORR2D +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 77%] Built target testBCUT +[ 77%] Built target testATF make -f Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testPBF.dir/DependInfo.cmake --color= @@ -6862,31 +6905,23 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 77%] Building CXX object 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../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 77%] Built target testAUTOCORR2D +[ 78%] Built target testBCUT make -f Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDFcustom.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors 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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/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/DaylightParser.cpp -[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionPickler.cpp -[ 78%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 78%] Built target RGroupDecomposition make -f Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testRDF.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu 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../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 78%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 79%] Built target testDescriptors +[ 79%] Built target testRDF make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake --color= @@ -6981,15 +7013,13 @@ make[4]: Entering directory 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'/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 79%] Built target testWHIM +[ 79%] Built target testMORSE make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/DependInfo.cmake --color= @@ -6998,11 +7028,13 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 80%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o cd 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 80%] Built target test3D +[ 80%] Built target testWHIM make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/DependInfo.cmake --color= @@ -7011,11 +7043,11 @@ make[4]: Entering directory 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/usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 80%] Built target testAUTOCORR3D +[ 80%] Built target testGETAWAY make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolAlign /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake --color= @@ -7037,10 +7069,34 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 80%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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 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-ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 80%] Built target testCoulombMat +make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/DependInfo.cmake --color= +[ 80%] Linking CXX executable testAUTOCORR3D +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/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 -DrdMolAlign_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolHash/hashfunctions.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7058,36 +7114,38 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Linking CXX executable testCoulombMat -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so 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/usr/lib/aarch64-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 +[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp +[ 80%] Linking CXX executable descriptorsTestCatch +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 81%] Built target testCoulombMat -make -f Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/build.make Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/depend +[ 80%] Built target descriptorsTestCatch +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend make[4]: Entering directory 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-I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp +[ 80%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp /build/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': /build/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:436:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 436 | python::list atomprops) { | ^ -[ 81%] Linking CXX executable descriptorsTestCatch -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2022.09.3 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../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 81%] Built target descriptorsTestCatch -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolHash /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 81%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolHash/hashfunctions.cpp +In file included from /usr/include/c++/12/bits/stl_algobase.h:64, + from /usr/include/c++/12/string:50, + from /build/rdkit-202209.3/Code/RDGeneral/Invariant.h:17, + from /build/rdkit-202209.3/Code/Numerics/Matrix.h:14, + from /build/rdkit-202209.3/Code/Numerics/SquareMatrix.h:14, + from /build/rdkit-202209.3/Code/Geometry/Transform3D.h:16, + from /build/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: +/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': +/build/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here +/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 741 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ In file included from /usr/include/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, @@ -7106,76 +7164,51 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_algobase.h:64, - from /usr/include/c++/12/string:50, - from /build/rdkit-202209.3/Code/RDGeneral/Invariant.h:17, - from /build/rdkit-202209.3/Code/Numerics/Matrix.h:14, - from /build/rdkit-202209.3/Code/Numerics/SquareMatrix.h:14, - from /build/rdkit-202209.3/Code/Geometry/Transform3D.h:16, - from /build/rdkit-202209.3/Code/GraphMol/MolAlign/AlignMolecules.h:14, - from /build/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: -/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': -/build/rdkit-202209.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here -/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 741 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/PNGParser.cpp +[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp +[ 81%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolHash/normalize.cpp [ 81%] Linking CXX executable testMolAlign cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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 ../../../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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 81%] Built target testMolAlign -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c 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-I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolHash/normalize.cpp -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp -[ 82%] Linking CXX executable testO3AAlign -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp -[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 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../../../lib/libRDKitMolAlign.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/libRDKitForceFieldHelpers.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitForceField.so.1.2022.09.3 ../../../lib/libRDKitOptimizer.so.1.2022.09.3 ../../../lib/libRDKitTrajectory.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 82%] Built target rdMolAlign +[ 81%] Built target testO3AAlign make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o +[ 81%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -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/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp [ 82%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2022.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 82%] Built target MolHash +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/PNGParser.cpp +[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Built target rdMolAlign make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake --color= @@ -7184,6 +7217,8 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 82%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/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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Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/CDXMLParser.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, @@ -7202,95 +7237,150 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 82%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp +[ 82%] Linking CXX executable rgroupCatchTests +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 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'/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Built target rgroupCatchTests +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolHash /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_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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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp +[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[ 82%] Linking CXX executable testRGroupDecompInternals +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Built target rdMolDescriptors +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolHash/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/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 -DrdMolHash_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Built target testRGroupDecompInternals +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/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp:10: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +[ 82%] Linking CXX executable testRGroupDecomp +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Built target testRGroupDecomp +[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitga.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Built target rdRGroupDecomposition +[ 82%] Linking CXX executable molHashCatchTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 82%] Built target molHashCatchTest +[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 83%] Built target rdMolHash +[ 83%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 ../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 82%] Built target ChemReactions +[ 83%] Built target ChemReactions make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/depend +make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend +make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ChemReactions /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake --color= -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend +make -f 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--color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build +make -f 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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../../../../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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Built target rdMolDescriptors -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend +make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ChemReactions /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2022.09.3 ../../../lib/libRDKitFMCS.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 +[ 83%] Building CXX object 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-ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp -[ 83%] Linking CXX executable testRGroupDecompInternals -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -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/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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl ../../../lib/libRDKitga.so.1.2022.09.3 +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/testReaction.cpp make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Built target testRGroupDecompInternals -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.cpp -In file included from /build/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:10: -/build/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_72()': -/build/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/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++); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitga.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Built target rdRGroupDecomposition -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend +[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o +[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp +[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp +[ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/MolStandardize.cpp +[ 84%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp +[ 84%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o +[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.cpp cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.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, @@ -7299,26 +7389,6 @@ 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/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -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/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/rdkit-202209.3/Code/Geometry/point.h:24, @@ -7329,56 +7399,6 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 83%] Linking CXX executable testReactionFingerprints -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Built target testReactionFingerprints -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolHash /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolHash/catch_tests.cpp -[ 83%] Linking CXX executable testRGroupDecomp -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Built target testRGroupDecomp -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolHash/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/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 -DrdMolHash_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -[ 83%] Linking CXX executable testEnumeration -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Built target testEnumeration -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Deprotect /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 83%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Deprotect/Deprotect.cpp -In file included from /usr/include/c++/12/bits/stl_algobase.h:64, - from /usr/include/c++/12/string:50, - from /build/rdkit-202209.3/Code/RDGeneral/Invariant.h:17, - from /build/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, - from /build/rdkit-202209.3/Code/GraphMol/QueryOps.h:19, - from /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:16: -/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double; _T2 = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': -/build/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:540:16: required from here -/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 741 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ In file included from /usr/include/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, @@ -7392,21 +7412,38 @@ 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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp:10: + from /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/Metal.cpp -[ 84%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -[ 84%] Linking CXX executable molHashCatchTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_serialization.so +/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/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:10: +/build/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp: In function 'void C_A_T_C_H_T_E_S_T_72()': +/build/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/rdkit-202209.3/Code/GraphMol/ChemReactions/catch_tests.cpp:1264:63: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 1264 | CHECK(mol->getProp("CDX_PRODUCT_ID") == i++); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /usr/include/c++/12/bits/stl_algobase.h:64, + from /usr/include/c++/12/string:50, + from /build/rdkit-202209.3/Code/RDGeneral/Invariant.h:17, + from /build/rdkit-202209.3/Code/GraphMol/RDKitBase.h:21, + from /build/rdkit-202209.3/Code/GraphMol/QueryOps.h:19, + from /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:16: +/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double; _T2 = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': +/build/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp:540:16: required from here +/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 741 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 84%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 84%] Built target rdMolHash +[ 84%] Built target Deprotect make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake --color= @@ -7415,8 +7452,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Wrap/rdmolops.cpp +[ 84%] Linking CXX executable testReactionFingerprints +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 84%] Built target molHashCatchTest +[ 84%] Built target testReactionFingerprints make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake --color= @@ -7425,22 +7465,8 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 84%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/Deprotect /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 85%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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 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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o 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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( | ^~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/Normalize.cpp -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/MolOps.cpp -[ 85%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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 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rxnTestCatch -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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/usr/lib/aarch64-linux-gnu/libboost_serialization.so -[ 85%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp +[ 84%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External 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-I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolEnumerator/PositionVariation.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, @@ -7498,15 +7522,21 @@ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 86%] Linking CXX executable deprotectTest +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7525,8 +7555,23 @@ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +[ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolEnumerator/LinkNode.cpp +[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp +[ 86%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o +cd 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CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp +[ 86%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /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 -DrdDeprotect_EXPORTS -I/build/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp +[ 86%] Linking CXX executable rxnTestCatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 86%] Built target rxnTestCatch +[ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/Validate.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, @@ -7534,18 +7579,17 @@ from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, - from /usr/include/boost/smart_ptr.hpp:19, - from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/Geometry/point.h:24, - from /build/rdkit-202209.3/Code/GraphMol/MolPickler.h:14, - from /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:34: + 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/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/Charge.cpp -[ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolEnumerator/LinkNode.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, @@ -7553,30 +7597,47 @@ 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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp:10: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/Geometry/point.h:24, + from /build/rdkit-202209.3/Code/GraphMol/MolPickler.h:14, + from /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:34: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.cpp [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp +[ 87%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 87%] 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/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/Charge.cpp [ 87%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /build/rdkit-202209.3/obj-aarch64-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 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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/usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 87%] Built target rdDeprotect -[ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/Fragment.cpp +make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 87%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -7592,8 +7653,28 @@ /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/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.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/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/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/DrawAnnotation.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp +[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', inlined from 'PyObject* RDKit::RunReactant(ChemicalReaction*, T, unsigned int) [with T = boost::python::api::object]' at /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:129:14: /usr/include/boost/smart_ptr/shared_ptr.hpp:416:66: warning: '*(const boost::shared_ptr*)((char*)& + offsetof(boost::python::extract >,boost::python::extract >::.boost::python::converter::extract_rvalue >::m_data.boost::python::converter::rvalue_from_python_data >::.boost::python::converter::rvalue_from_python_storage >::storage)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] @@ -7614,32 +7695,6 @@ /build/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/FragmentCatalogParams.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp -[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp -[ 88%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/Wrap/ChiralityOps.cpp -[ 88%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolEnumerator /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/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, @@ -7658,91 +7713,44 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp -[ 90%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security 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../../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 90%] Built target rdChemReactions -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 90%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp -[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawAnnotation.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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/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( - | ^~~~~~~~~~~~~~~~~~~~ -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp -[ 90%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -[ 90%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd 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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/rdkit-202209.3/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 88%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawShape.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp -[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_64BIT_BUILD 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/build/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp -[ 90%] Linking CXX executable testReaction -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_serialization.so +[ 88%] Built target rdMolEnumerator +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/Fragment.cpp +[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp +[ 88%] Linking CXX executable testMolEnumerator +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp In file included from /usr/include/c++/12/bits/stl_algobase.h:64, from /usr/include/c++/12/string:50, from /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawText.h:19, @@ -7752,16 +7760,116 @@ /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK 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CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextJS.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD 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CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +[ 92%] Linking CXX executable testReaction +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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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/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/rdkit-202209.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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 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../../../lib/libRDKitMolDraw2D.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libcairo.so +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 92%] Built target MolDraw2D +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/build/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/usr/include/freetype2 -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +In file included from /usr/include/c++/12/bits/stl_algobase.h:64, + from /usr/include/c++/12/bits/specfun.h:45, + from /usr/include/c++/12/cmath:1935, + from /build/rdkit-202209.3/Code/RDGeneral/types.h:21, + from /build/rdkit-202209.3/Code/RDGeneral/utils.h:15, + from /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:12: +/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': +/build/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:1600:46: required from here +/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 741 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +In file included from /usr/include/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/rdkit-202209.3/Code/RDBoost/python.h:3, + from /build/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( + | ^~~~~~~~~~~~~~~~~~~~ [ 92%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so @@ -7769,37 +7877,42 @@ make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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 -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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-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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 93%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake --color= @@ -7816,6 +7934,11 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/testTautomer.cpp +[ 94%] Linking CXX executable molNormalizeTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 94%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake --color= @@ -7824,99 +7947,59 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/test2.cpp -[ 94%] Linking CXX executable molValidateTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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 molChargeTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 94%] Built target molValidateTest +[ 95%] Built target molChargeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o +[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/testFragment.cpp -[ 94%] Linking CXX executable molNormalizeTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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 shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libboost_serialization.so ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 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../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitMolTransforms.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2022.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 94%] Built target molNormalizeTest +[ 95%] Built target TautomerQuery make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o +[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/catch_tests.cpp -[ 94%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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'/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 94%] Built target TautomerQuery +[ 95%] Built target molStandardizeTest make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 94%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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 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-I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp -cd /build/rdkit-202209.3/obj-aarch64-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 +[ 95%] Linking CXX executable molStandardizeSmallTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 95%] Linking CXX executable molChargeTest -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -[ 95%] Built target MolDraw2D +[ 95%] Built target molStandardizeSmallTest make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork 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/usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Built target molStandardizeSmallTest -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -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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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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/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("") - | ^~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX executable molFragmentTest cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 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/usr/lib/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' [ 96%] Built target molFragmentTest -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake --color= +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/TautomerQuery /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/usr/include/freetype2 -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolDraw2D/catch_tests.cpp +[ 96%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/TautomerQuery/catch_tests.cpp +[ 96%] Linking CXX executable moldraw2DTest1 +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so [ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp -In file included from /usr/include/c++/12/bits/stl_algobase.h:64, - from /usr/include/c++/12/bits/specfun.h:45, - from /usr/include/c++/12/cmath:1935, - from /build/rdkit-202209.3/Code/RDGeneral/types.h:21, - from /build/rdkit-202209.3/Code/RDGeneral/utils.h:15, - from /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:12: -/usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double]': -/build/rdkit-202209.3/Code/GraphMol/MolDraw2D/test1.cpp:1600:46: required from here -/usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 741 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 96%] Built target moldraw2DTest1 +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 96%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp [ 96%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' [ 96%] Built target ScaffoldNetwork -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp -[ 96%] Linking CXX executable tautomerQueryTestCatch -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Built target tautomerQueryTestCatch -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake --color= +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +[ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.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, @@ -8028,35 +8083,21 @@ 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/rdkit-202209.3/Code/RDBoost/python.h:3, - from /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:11: + from /usr/include/boost/smart_ptr.hpp:19, + from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/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( | ^~~~~~~~~~~~~~~~~~~~ -[ 96%] Linking CXX executable molTautomerTest -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 -[ 96%] Linking CXX executable molStandardizeCatchTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Built target molTautomerTest -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build -make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 96%] Built target molStandardizeCatchTest +[ 96%] Built target rdMolDraw2D make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake --color= @@ -8065,26 +8106,33 @@ make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd 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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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 98%] Built target rdTautomerQuery +[ 97%] Built target molStandardizeCatchTest make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o +[ 97%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -[ 98%] Linking CXX executable moldraw2DRxnTest1 -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so +[ 97%] Linking CXX executable tautomerQueryTestCatch +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 98%] Built target moldraw2DRxnTest1 -[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +[ 97%] Built target tautomerQueryTestCatch +[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp +[ 97%] Linking CXX executable molTautomerTest +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 ../../../lib/libRDKitDepictor.so.1.2022.09.3 ../../../lib/libRDKitMolAlign.so.1.2022.09.3 ../../../lib/libRDKitSmilesParse.so.1.2022.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2022.09.3 ../../../lib/libRDKitAlignment.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[ 97%] Built target molTautomerTest +[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, @@ -8103,8 +8151,13 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat 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moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so 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/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF 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Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/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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+cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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 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../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/aarch64-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 -[ 99%] Linking CXX executable moldraw2DTest1 -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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../../../lib/libRDKitSubgraphs.so.1.2022.09.3 ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 99%] Built target moldraw2DTest1 -[ 99%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o +[100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o cd /build/rdkit-202209.3/obj-aarch64-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 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/build/rdkit-202209.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.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, @@ -8216,23 +8227,6 @@ 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/rdkit-202209.3/Code/Numerics/Vector.h:23, - from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: -/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' - 36 | BOOST_PRAGMA_MESSAGE( - | ^~~~~~~~~~~~~~~~~~~~ -/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' - 13 | BOOST_HEADER_DEPRECATED("") - | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, - from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, - from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, - from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, - from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, - from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, - from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, @@ -8258,19 +8252,55 @@ from /usr/include/boost/smart_ptr.hpp:19, from /build/rdkit-202209.3/Code/Numerics/Vector.h:23, from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, - from /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.h:36, - from /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp:32: + from /build/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ -[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +[100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so 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-E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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 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../../../lib/libRDKitDataStructs.so.1.2022.09.3 ../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[100%] Built target testScaffoldNetwork +[100%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=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/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[100%] 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 -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +cd /build/rdkit-202209.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/rdkit-202209.3 /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/catch2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/rdkit-202209.3/Code -I/build/rdkit-202209.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-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/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp -[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.so.1.2022.09.3 ../../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/aarch64-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 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-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, @@ -8289,23 +8319,30 @@ /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( | ^~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 99%] Built target rdMolDraw2D -[ 99%] Linking CXX executable substructLibraryCatchTest +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/rdkit-202209.3/Code/Numerics/Vector.h:23, + from /build/rdkit-202209.3/Code/RDBoost/Wrap.h:17, + from /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.h:36, + from /build/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp:32: +/usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' + 36 | BOOST_PRAGMA_MESSAGE( + | ^~~~~~~~~~~~~~~~~~~~ +/usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' + 13 | BOOST_HEADER_DEPRECATED("") + | ^~~~~~~~~~~~~~~~~~~~~~~ +[100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitGenericGroups.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl +[100%] Linking CXX executable substructLibraryCatchTest cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitChemTransforms.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[ 99%] Built target substructLibraryCatchTest -[100%] Linking CXX executable moldraw2DTestCatch -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2022.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2022.09.3 ../../../lib/libRDKitChemReactions.so.1.2022.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2022.09.3 ../../../lib/libRDKitCatalogs.so.1.2022.09.3 ../../../lib/libRDKitDescriptors.so.1.2022.09.3 ../../../lib/libRDKitPartialCharges.so.1.2022.09.3 ../../../lib/libRDKitFingerprints.so.1.2022.09.3 ../../../lib/libRDKitFileParsers.so.1.2022.09.3 /usr/lib/aarch64-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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-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/libRDKitEigenSolvers.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2022.09.3 /usr/lib/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' -[100%] Built target moldraw2DTestCatch -[100%] Linking CXX executable substructLibraryTest -cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so 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../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl -make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' -[100%] Built target substructLibraryTest /build/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/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, @@ -8333,11 +8370,15 @@ | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 | numThreads); | ~~~~~~~~~~~ -[100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake 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/usr/lib/aarch64-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/aarch64-linux-gnu/libboost_serialization.so ../../../../lib/libRDKitRDGeometryLib.so.1.2022.09.3 ../../../../lib/libRDKitDataStructs.so.1.2022.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' [100%] Built target rdMolStandardize +make[4]: Leaving directory '/build/rdkit-202209.3/obj-aarch64-linux-gnu' +[100%] Built target substructLibraryCatchTest +[100%] Linking CXX executable substructLibraryTest +cd /build/rdkit-202209.3/obj-aarch64-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/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/aarch64-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/rdkit-202209.3/obj-aarch64-linux-gnu' +[100%] Built target substructLibraryTest [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/rdkit-202209.3=. -fstack-protector-strong -Wformat -Werror=format-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/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2022.09.3 ../../../../lib/libRDKitRDBoost.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/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-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/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 /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2022.09.3 -ldl @@ -13833,7 +13874,7 @@ /build/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:1444: WARNING: None:any reference target not found: ./C++Examples/example15.cpp /build/rdkit-202209.3/Docs/Book/GettingStartedInC++.md:1472: WARNING: None:any reference target not found: ./C++Examples/example16.cpp /build/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/rdkit-202209.3/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known /build/rdkit-202209.3/Docs/Book/Install.md:: WARNING: Pygments lexer name 'shellsession' is not known @@ -16378,8 +16419,8 @@ 8: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/testDataStructs 8: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs 8: Test timeout computed to be: 1500 -3: [20:16:46] Testing Github940: property dictionaries leaking memory -3: [20:16:46] done +3: [07:09:15] Testing Github940: property dictionaries leaking memory +3: [07:09:15] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect @@ -16396,43 +16437,43 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [20:16:46] +5: [07:09:15] 5: ----------------------------------------- -5: [20:16:46] Finished: testPushAndPop() -5: [20:16:46] +5: [07:09:15] Finished: testPushAndPop() +5: [07:09:15] 5: ----------------------------------------- -5: [20:16:46] +5: [07:09:15] 5: ----------------------------------------- 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [20:16:46] should not be silent -7: [20:16:46] should not be silent -7: [20:16:46] should not be silent -7: [20:16:46] should not be silent -7: [20:16:46] should not be silent -7: [20:16:46] should not be silent -7: [20:16:46] should not be silent -7: [20:16:46] should not be silent -7: [20:16:46] should not be silent -7: =============================================================================== -7: All tests passed (24 assertions in 2 test cases) -7: - 1/208 Test #4: testRDValue ............................ Passed 0.09 sec + 1/208 Test #4: testRDValue ............................ Passed 0.01 sec test 9 Start 9: testFPB 9: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/testFPB 9: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs 9: Test timeout computed to be: 1500 - 2/208 Test #6: dictTestsCatch ......................... Passed 0.09 sec + 2/208 Test #6: dictTestsCatch ......................... Passed 0.01 sec test 10 Start 10: testMultiFPB 10: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/testMultiFPB 10: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs 10: Test timeout computed to be: 1500 - 3/208 Test #7: logTestsCatch .......................... Passed 0.10 sec +7: [07:09:15] should not be silent +7: [07:09:15] should not be silent +7: [07:09:15] should not be silent +7: [07:09:15] should not be silent +7: [07:09:15] should not be silent +7: [07:09:15] should not be silent +7: [07:09:15] should not be silent +7: [07:09:15] should not be silent +7: [07:09:15] should not be silent +7: =============================================================================== +7: All tests passed (24 assertions in 2 test cases) +7: + 3/208 Test #7: logTestsCatch .......................... Passed 0.01 sec test 11 Start 11: pyBV @@ -16455,14 +16496,14 @@ 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 - 4/208 Test #8: testDataStructs ........................ Passed 0.10 sec + 4/208 Test #8: testDataStructs ........................ Passed 0.01 sec test 12 Start 12: pyDiscreteValueVect 12: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/DataStructs/Wrap/testDiscreteValueVect.py" 12: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/Wrap 12: Test timeout computed to be: 1500 - 5/208 Test #9: testFPB ................................ Passed 0.07 sec + 5/208 Test #9: testFPB ................................ Passed 0.01 sec test 13 Start 13: pySparseIntVect @@ -16503,6 +16544,13 @@ 1: 7 1 1 0 1: M END 1: + 6/208 Test #10: testMultiFPB ........................... Passed 0.02 sec +test 14 + Start 14: pyFPB + +14: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/DataStructs/Wrap/testFPB.py" +14: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/Wrap +14: Test timeout computed to be: 1500 1: templated 1: RDKit 2D 1: @@ -16862,13 +16910,6 @@ 1: 5 7 1 0 1: M END 1: - 6/208 Test #10: testMultiFPB ........................... Passed 0.17 sec -test 14 - Start 14: pyFPB - -14: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/DataStructs/Wrap/testFPB.py" -14: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataStructs/Wrap -14: Test timeout computed to be: 1500 1: templated 1: RDKit 2D 1: @@ -16933,12 +16974,59 @@ 1: 2 5 1 0 1: M END 1: -3: static boost any:0.529607 s 12: ...... 12: ---------------------------------------------------------------------- -12: Ran 6 tests in 0.017s +12: Ran 6 tests in 0.005s 12: 12: OK +13: ......... +13: ---------------------------------------------------------------------- +13: Ran 9 tests in 0.015s +13: +13: OK +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.025s +14: +14: OK + 7/208 Test #12: pyDiscreteValueVect .................... Passed 0.48 sec +test 15 + Start 15: testTransforms + +15: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/testTransforms +15: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry +15: Test timeout computed to be: 1500 +15: **************************************** +15: testPointND +15: **************************************** +15: testPointOps3D +15: **************************************** +15: testPointOps2D +15: **************************************** +15: test12D +15: ref1: 0.929646 3.57222 ref2: 1.73354 2.08102 +15: pt1: 1.70067 1.47912 pt2: 3.48522 1.93993 +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: **************************************** + 8/208 Test #15: testTransforms ......................... Passed 0.01 sec +test 16 + Start 16: testGrid + +16: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/testGrid +16: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry +16: Test timeout computed to be: 1500 1: cyclosporine a 1: RDKit 2D 1: @@ -17115,13 +17203,6 @@ 1: 46 3 1 0 1: M END 1: - 7/208 Test #12: pyDiscreteValueVect .................... Passed 1.77 sec -test 15 - Start 15: testTransforms - -15: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/testTransforms -15: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry -15: Test timeout computed to be: 1500 1: single-double 1: RDKit 2D 1: @@ -17186,37 +17267,11 @@ 1: 9 10 1 0 1: M END 1: -15: **************************************** -15: testPointND -15: **************************************** -15: testPointOps3D -15: **************************************** -15: testPointOps2D -15: **************************************** -15: test12D -15: ref1: 1.78188 3.99635 ref2: 0.183051 1.91856 -15: pt1: 4.22464 3.09095 pt2: 3.96297 0.826638 -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: **************************************** - 8/208 Test #15: testTransforms ......................... Passed 0.03 sec -test 16 - Start 16: testGrid - -16: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/testGrid -16: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry -16: Test timeout computed to be: 1500 +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.061s +2: +2: OK 1: admntn 1: RDKit 2D 1: @@ -17245,16 +17300,7 @@ 1: 10 2 1 0 1: M END 1: -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.077s -14: -14: OK -13: ......... -13: ---------------------------------------------------------------------- -13: Ran 9 tests in 0.068s -13: -13: OK +3: static boost any:0.529963 s 16: *********************************************************** 16: Testing Grid 16: --------------------------------- @@ -17272,7 +17318,7 @@ 16: --------------------------------- 16: testUniformGridIndexing 16: - 9/208 Test #16: testGrid ............................... Passed 0.17 sec + 9/208 Test #16: testGrid ............................... Passed 0.04 sec test 17 Start 17: geometryTestsCatch @@ -17282,55 +17328,44 @@ 17: =============================================================================== 17: All tests passed (50 assertions in 5 test cases) 17: - 10/208 Test #1: testCoordGen ........................... Passed 2.20 sec + 10/208 Test #13: pySparseIntVect ........................ Passed 0.55 sec test 18 Start 18: testPyGeometry 18: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/Geometry/Wrap/testGeometry.py" 18: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap 18: Test timeout computed to be: 1500 - 11/208 Test #17: geometryTestsCatch ..................... Passed 0.10 sec + 11/208 Test #17: geometryTestsCatch ..................... Passed 0.02 sec test 19 Start 19: testMatrices 19: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/testMatrices 19: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics 19: Test timeout computed to be: 1500 - 12/208 Test #14: pyFPB .................................. Passed 1.97 sec +19: [07:09:16] ----------------------------------------- +19: [07:09:16] Testing RDNumerics: vectors and matrices Code +19: [07:09:16] --------------------------------------- +19: [07:09:16] test1Vector +19: [07:09:16] --------------------------------------- +19: [07:09:16] test2Matrix +19: [07:09:16] --------------------------------------- +19: [07:09:16] test3SquareMatrix +19: [07:09:16] --------------------------------------- +19: [07:09:16] test4SymmMatrix + 12/208 Test #19: testMatrices ........................... Passed 0.01 sec test 20 Start 20: testConrec 20: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/testConrec 20: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics 20: Test timeout computed to be: 1500 -19: [20:16:48] ----------------------------------------- -19: [20:16:48] Testing RDNumerics: vectors and matrices Code -19: [20:16:48] --------------------------------------- -19: [20:16:48] test1Vector -19: [20:16:48] --------------------------------------- -19: [20:16:48] test2Matrix -19: [20:16:48] --------------------------------------- -19: [20:16:48] test3SquareMatrix -19: [20:16:48] --------------------------------------- -19: [20:16:48] test4SymmMatrix - 13/208 Test #19: testMatrices ........................... Passed 0.03 sec + 13/208 Test #14: pyFPB .................................. Passed 0.55 sec test 21 Start 21: testAlignment 21: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment 21: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment 21: Test timeout computed to be: 1500 -20: =============================================================================== -20: test cases: 1 | 1 passed -20: assertions: - none - -20: - 14/208 Test #20: testConrec ............................. Passed 0.03 sec -test 22 - Start 22: pyAlignment - -22: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py" -22: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap -22: Test timeout computed to be: 1500 21: ----------------------------------------- 21: Testing Alignment Code 21: --------------------------------------- @@ -17342,31 +17377,44 @@ 21: --------------------------------------- 21: testReflection 21: --------------------------------------- - 15/208 Test #21: testAlignment .......................... Passed 0.04 sec + 14/208 Test #1: testCoordGen ........................... Passed 0.60 sec +test 22 + Start 22: pyAlignment + +22: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/Numerics/Alignment/Wrap/testAlignment.py" +22: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap +22: Test timeout computed to be: 1500 +20: =============================================================================== +20: test cases: 1 | 1 passed +20: assertions: - none - +20: + 15/208 Test #20: testConrec ............................. Passed 0.02 sec test 23 Start 23: testOptimizer 23: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer 23: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer 23: Test timeout computed to be: 1500 -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.203s -2: -2: OK + 16/208 Test #21: testAlignment .......................... Passed 0.02 sec +test 24 + Start 24: testUFFForceField + +24: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField +24: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/UFF +24: Test timeout computed to be: 1500 23: ------------------------------------- 23: Testing linear search. 23: done 23: ------------------------------------- 23: Testing BFGS optimization. 23: done - 16/208 Test #23: testOptimizer .......................... Passed 0.03 sec -test 24 - Start 24: testUFFForceField + 17/208 Test #23: testOptimizer .......................... Passed 0.01 sec +test 25 + Start 25: testMMFFForceField -24: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField -24: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/UFF -24: Test timeout computed to be: 1500 +25: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +25: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF +25: Test timeout computed to be: 1500 24: ------------------------------------- 24: Unit tests for force field basics. 24: done @@ -17413,16 +17461,9 @@ 24: done 24: ------------------------------------- 24: Unit tests for all UFF constraint terms. - 17/208 Test #13: pySparseIntVect ........................ Passed 2.28 sec -test 25 - Start 25: testMMFFForceField - -25: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -25: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF -25: Test timeout computed to be: 1500 25: ------------------------------------- 25: Official MMFF validation suite. - 18/208 Test #2: pyCoordGen ............................. Passed 2.79 sec + 18/208 Test #2: pyCoordGen ............................. Passed 0.65 sec test 26 Start 26: pyForceFieldConstraints @@ -17481,11 +17522,17 @@ 22: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 22: 22: ---------------------------------------------------------------------- -22: Ran 5 tests in 0.016s +22: Ran 5 tests in 0.004s 22: 22: FAILED (errors=3) 22: Testing Alignment Wrapper code: - 19/208 Test #22: pyAlignment ............................***Failed 1.45 sec +18: ........... +18: ---------------------------------------------------------------------- +18: Ran 11 tests in 0.045s +18: +18: OK +18: Testing Geometry wrapper + 19/208 Test #22: pyAlignment ............................***Failed 0.50 sec EEE.. ====================================================================== ERROR: test1Basic (__main__.TestCase.test1Basic) @@ -17530,7 +17577,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 5 tests in 0.016s +Ran 5 tests in 0.004s FAILED (errors=3) Testing Alignment Wrapper code: @@ -17552,34 +17599,32 @@ 27: 1 1 1 0 27: *********************************************************** 27: - 20/208 Test #27: testDistGeom ........................... Passed 0.04 sec + 20/208 Test #27: testDistGeom ........................... Passed 0.02 sec test 28 Start 28: pyDistGeom 28: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/DistGeom/Wrap/rough_test.py" 28: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap 28: Test timeout computed to be: 1500 -18: ........... -18: ---------------------------------------------------------------------- -18: Ran 11 tests in 0.179s -18: -18: OK -18: Testing Geometry wrapper 24: done - 21/208 Test #24: testUFFForceField ...................... Passed 2.00 sec + 21/208 Test #24: testUFFForceField ...................... Passed 0.52 sec test 29 Start 29: graphmolTest1 29: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 29: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 29: Test timeout computed to be: 1500 - 22/208 Test #18: testPyGeometry ......................... Passed 2.29 sec + 22/208 Test #18: testPyGeometry ......................... Passed 0.56 sec test 30 Start 30: graphmolcpTest 30: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest 30: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 30: Test timeout computed to be: 1500 +30: +30: +30: +30: COPY 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 @@ -17589,7 +17634,7 @@ 29: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 29: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 29: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 -29: 8 22 Ti chg: 0 deg: 1 exp: [20:16:50] +29: 8 22 Ti chg: 0 deg: 1 exp: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17607,7 +17652,7 @@ 29: 4 5->6 order: 3 conj?: 0 aromatic?: 0 29: 5 6->7 order: 1 conj?: 0 aromatic?: 0 29: 6 7->8 order: 2 conj?: 0 aromatic?: 0 -29: [20:16:50] +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17616,7 +17661,7 @@ 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: -29: [20:16:50] +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17625,7 +17670,7 @@ 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: -29: [20:16:50] +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17634,7 +17679,7 @@ 29: Failed Expression: atomIdx1 != atomIdx2 29: **** 29: -29: [20:16:50] +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17643,7 +17688,7 @@ 29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 29: **** 29: -29: [20:16:50] +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17652,20 +17697,17 @@ 29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 29: **** 29: -29: [20:16:50] Explicit valence for atom # 0 B, 4, is greater than permitted -29: [20:16:50] Explicit valence for atom # 0 B, 5, is greater than permitted -30: -30: -30: -30: COPY - 23/208 Test #30: graphmolcpTest ......................... Passed 0.14 sec +29: [07:09:16] Explicit valence for atom # 0 B, 4, is greater than permitted + 23/208 Test #30: graphmolcpTest ......................... Passed 0.03 sec test 31 Start 31: graphmolqueryTest 31: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest 31: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 31: Test timeout computed to be: 1500 -29: [20:16:50] +29: [07:09:16] Explicit valence for atom # 0 B, 5, is greater than permitted +31: [07:09:16] ---------------------- Test1 +29: [07:09:16] 29: 29: **** 29: Post-condition Violation @@ -17674,50 +17716,42 @@ 29: Failed Expression: anum > -1 29: **** 29: -29: [20:16:50] ------------------------------------- -29: [20:16:50] Test github381: thread-safe initialization of the periodic table -31: [20:16:50] ---------------------- Test1 -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test2 -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test3 -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test4 -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test5 -31: [20:16:50] Done! -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test issue 2892580 -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test github issue 53: query molecules not matching [R] -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test queries using qualifiers instead of == -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test extra atom queries -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test extra bond queries -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test num heteroatom neighbor queries -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test atom type queries -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -31: [20:16:50] Done! -31: [20:16:50] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -31: [20:16:50] Done! - 24/208 Test #31: graphmolqueryTest ...................... Passed 0.19 sec -test 32 - Start 32: graphmolMolOpsTest - -32: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -32: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol -32: Test timeout computed to be: 1500 -29: [20:16:50] done -29: [20:16:50] ------------------------------------- -29: [20:16:50] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [20:16:50] +29: [07:09:16] ------------------------------------- +29: [07:09:16] Test github381: thread-safe initialization of the periodic table +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test2 +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test3 +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test4 +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test5 +31: [07:09:16] Done! +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test issue 2892580 +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test github issue 53: query molecules not matching [R] +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test queries using qualifiers instead of == +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test extra atom queries +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test extra bond queries +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test num heteroatom neighbor queries +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test atom type queries +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +31: [07:09:16] Done! +31: [07:09:16] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +31: [07:09:16] Done! +29: [07:09:16] done +29: [07:09:16] ------------------------------------- +29: [07:09:16] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17726,7 +17760,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [20:16:50] +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17735,10 +17769,10 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [20:16:50] done -29: [20:16:50] ------------------------------------- -29: [20:16:50] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [20:16:50] +29: [07:09:16] done +29: [07:09:16] ------------------------------------- +29: [07:09:16] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17747,7 +17781,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [20:16:50] +29: [07:09:16] 29: 29: **** 29: Pre-condition Violation @@ -17756,27 +17790,58 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [20:16:50] done -29: [20:16:50] ------------------------------------- -29: [20:16:50] Test github1453: RWMol.clear() should reset the numBonds count. -29: [20:16:50] done -29: [20:16:50] ------------------------------------- -29: [20:16:50] Test range-based for loops. -29: [20:16:50] done -29: [20:16:50] ------------------------------------- -29: [20:16:50] Test github1642: Atom index type is too low for big molecules. +29: [07:09:16] done +29: [07:09:16] ------------------------------------- +29: [07:09:16] Test github1453: RWMol.clear() should reset the numBonds count. +29: [07:09:16] done +29: [07:09:16] ------------------------------------- +29: [07:09:16] Test range-based for loops. +29: [07:09:16] done +29: [07:09:16] ------------------------------------- +29: [07:09:16] Test github1642: Atom index type is too low for big molecules. +26: ...[07:09:16] Warning: molecule is tagged as 3D, but all Z coords are zero + 24/208 Test #31: graphmolqueryTest ...................... Passed 0.04 sec +test 32 + Start 32: graphmolMolOpsTest + +32: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +32: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol +32: Test timeout computed to be: 1500 +26: [07:09:16] Molecule does not have explicit Hs. Consider calling AddHs() +26: [07:09:16] +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: 32: 1 1 2 32: 1 1 1 32: 2 1 0.75 32: path: 2 -32: [20:16:51] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. -32: [20:16:51] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. -32: [20:16:51] Explicit valence for atom # 0 B, 5, is greater than permitted -32: [20:16:51] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [20:16:51] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [20:16:51] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [20:16:51] Explicit valence for atom # 1 Si, 7, is greater than permitted -3: dynamic boost any:1.17092 s +32: [07:09:17] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. +32: [07:09:17] Warning: conflicting stereochemistry at atom 10 ignored. by rule 1a. +32: [07:09:17] Explicit valence for atom # 0 B, 5, is greater than permitted +32: [07:09:17] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [07:09:17] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [07:09:17] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [07:09:17] Explicit valence for atom # 1 Si, 7, is greater than permitted +32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +32: [07:09:17] non-ring atom 0 marked aromatic +32: [07:09:17] non-ring atom 0 marked aromatic +32: [07:09:17] Conflicting single bond directions around double bond at index 17. +32: [07:09:17] 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 +32: done 28: EEEEEE 28: ====================================================================== 28: ERROR: test1SmoothPass (__main__.TestCase.test1SmoothPass) @@ -17863,14 +17928,19 @@ 28: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 28: 28: ---------------------------------------------------------------------- -28: Ran 6 tests in 0.016s +28: Ran 6 tests in 0.007s 28: 28: FAILED (errors=6) -3: static RDAny:0.058859 s -32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -26: ...[20:16:51] Warning: molecule is tagged as 3D, but all Z coords are zero -26: [20:16:51] Molecule does not have explicit Hs. Consider calling AddHs() -26: [20:16:51] +32: starting sanitization +32: done +32: starting ring finding +32: done +32: starting ring finding +32: done +26: ......[07:09:17] Warning: molecule is tagged as 3D, but all Z coords are zero +32: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 +26: [07:09:17] Molecule does not have explicit Hs. Consider calling AddHs() +26: [07:09:17] 26: 26: **** 26: Invariant Violation @@ -17879,7 +17949,15 @@ 26: Failed Expression: status >= 0 26: **** 26: - 25/208 Test #28: pyDistGeom .............................***Failed 1.94 sec +32: [07:09:17] WARNING: not removing hydrogen atom with dummy atom neighbors +32: ------------------------------- +32: [07:09:17] Explicit valence for atom # 0 N, 4, is greater than permitted +32: [07:09:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [07:09:17] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +32: [07:09:17] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [07:09:17] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +32: [07:09:17] WARNING: not removing hydrogen atom with dummy atom neighbors + 25/208 Test #28: pyDistGeom .............................***Failed 0.51 sec EEEEEE ====================================================================== ERROR: test1SmoothPass (__main__.TestCase.test1SmoothPass) @@ -17966,7 +18044,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 6 tests in 0.016s +Ran 6 tests in 0.007s FAILED (errors=6) @@ -17976,81 +18054,57 @@ 33: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality 33: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 -32: [20:16:51] non-ring atom 0 marked aromatic -32: [20:16:51] non-ring atom 0 marked aromatic -32: [20:16:51] Conflicting single bond directions around double bond at index 17. -32: [20:16:51] 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 33: -------------------------- 33: -------------------------- 33: C/C=C/C(C)Cl -32: done -32: starting sanitization -32: done -32: starting ring finding -32: done -32: starting ring finding -32: done -32: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -32: [20:16:52] WARNING: not removing hydrogen atom with dummy atom neighbors -32: ------------------------------- -32: [20:16:52] Explicit valence for atom # 0 N, 4, is greater than permitted -32: [20:16:52] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [20:16:52] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -32: [20:16:52] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [20:16:52] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -33: [20:16:52] Conflicting single bond directions around double bond at index 2. -33: [20:16:52] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [20:16:52] Conflicting single bond directions around double bond at index 4. -33: [20:16:52] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [20:16:52] Conflicting single bond directions around double bond at index 15. -33: [20:16:52] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [20:16:52] Conflicting single bond directions around double bond at index 2. -33: [20:16:52] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [20:16:52] Conflicting single bond directions around double bond at index 1. -33: [20:16:52] BondStereo set to STEREONONE and single bond directions set to NONE. -32: [20:16:52] WARNING: not removing hydrogen atom with dummy atom neighbors +33: [07:09:17] Conflicting single bond directions around double bond at index 2. +33: [07:09:17] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [07:09:17] Conflicting single bond directions around double bond at index 4. +33: [07:09:17] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [07:09:17] Conflicting single bond directions around double bond at index 15. +33: [07:09:17] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [07:09:17] Conflicting single bond directions around double bond at index 2. +33: [07:09:17] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [07:09:17] Conflicting single bond directions around double bond at index 1. +33: [07:09:17] BondStereo set to STEREONONE and single bond directions set to NONE. 33: -------------------------------------------------- - 26/208 Test #33: graphmoltestChirality .................. Passed 0.59 sec + 26/208 Test #33: graphmoltestChirality .................. Passed 0.10 sec test 34 Start 34: graphmoltestPickler 34: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler 34: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 -26: ......[20:16:52] Warning: molecule is tagged as 3D, but all Z coords are zero -26: [20:16:52] Molecule does not have explicit Hs. Consider calling AddHs() -26: [20:16:52] -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: -34: [20:16:52] ------------------------------------- -34: [20:16:52] Testing String Pickle Roundtrips. +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing String Pickle Roundtrips. 26: ... 26: ---------------------------------------------------------------------- -26: Ran 12 tests in 1.629s +26: Ran 12 tests in 0.674s 26: 26: OK -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing reading existing pickle file (v2). -3: dynamic RDAny:0.57214 s -3: static RDValue:1e-06 s -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing combining molecules using pickles. +3: dynamic boost any:1.22126 s +3: static RDAny:0.059504 s +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing reading existing pickle file (v2). + 27/208 Test #26: pyForceFieldConstraints ................ Passed 1.25 sec +test 35 + Start 35: graphmoltestPicklerGlobalSetting + +35: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +35: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 +35: [07:09:17] done + 28/208 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.04 sec +test 36 + Start 36: graphmolIterTest + +36: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest +36: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] 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 @@ -18067,98 +18121,53 @@ 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: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing Issue164: Roundtrip Pickle Failure. - 27/208 Test #26: pyForceFieldConstraints ................ Passed 4.60 sec -test 35 - Start 35: graphmoltestPicklerGlobalSetting +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing Issue164: Roundtrip Pickle Failure. + 29/208 Test #36: graphmolIterTest ....................... Passed 0.04 sec +test 37 + Start 37: hanoiTest -35: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -35: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -3: dynamic RDValue:0.046385 s -3: deleted! -3: [20:16:53] ------------------------------------- -3: [20:16:53] Testing String Pickle Roundtrips. -3: [20:16:53] done -3: [20:16:53] ------------------------------------- -3: [20:16:53] Testing conversion of vect to string. -3: [20:16:53] done -3: [20:16:53] ------------------------------------- -3: [20:16:53] Testing returning const references. -3: [20:16:53] any cast -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing Issue219: Pickle Failure with Conformations. -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing Issue220: Pickle problems with bond stereochemistry. -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing query serialization. -3: [20:16:53] done: 0.001846 300000 -3: [20:16:53] copy -3: [20:16:53] done: 0.001797 300000 -3: [20:16:53] ref -34: [20:16:53] C=[$(C=O)] -34: [20:16:53] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -3: [20:16:53] done: 0.001843 300000 -3: [20:16:53] dict -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing radical handling in pickles. -34: [20:16:53] done -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing sf.net issue 2788233. -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing sf.net issue 3202580. +37: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest +37: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing Issue219: Pickle Failure with Conformations. +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing Issue220: Pickle problems with bond stereochemistry. +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing query serialization. +34: [07:09:17] C=[$(C=O)] +34: [07:09:17] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing radical handling in pickles. +34: [07:09:17] done +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing sf.net issue 2788233. +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing sf.net issue 3202580. 34: mass! 13.0034 -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing sf.net issue 3316407. -3: [20:16:53] done: 0.006882 300000 -3: [20:16:53] ref with hasVal -3: [20:16:53] done: 0.002466 300000 -3: [20:16:53] done -3: [20:16:53] ------------------------------------- -3: [20:16:53] Testing dict update. -3: [20:16:53] done -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -3: deleted! -34: [20:16:53] done -34: [20:16:53] ------------------------------------- -34: [20:16:53] Testing sf.net issue 3496759. +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing sf.net issue 3316407. +34: [07:09:17] done +34: [07:09:17] ------------------------------------- +34: [07:09:17] Testing sf.net issue 3496759. 34: smi match: *C *C 34: smi match: **=* **=* 34: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O 34: smi match: *OS(=O)OC *OS(=O)OC 34: smi match: *S(=O)(=O)OC *S(=O)(=O)OC - 28/208 Test #3: testDict ............................... Passed 7.52 sec -test 36 - Start 36: graphmolIterTest - -36: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest -36: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -35: [20:16:53] done 34: smi match: O=COC=O O=COC=O 34: smi match: OO OO 34: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 34: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 - 29/208 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.15 sec -test 37 - Start 37: hanoiTest - -37: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest -37: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 34: smi match: nnnOC=O nnnOC=O 34: smi match: *=C=N *=C=N 34: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F @@ -18202,13 +18211,6 @@ 34: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 34: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 34: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 - 30/208 Test #36: graphmolIterTest ....................... Passed 0.14 sec -test 38 - Start 38: graphmolMemTest1 - -38: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 -38: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 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 @@ -18233,13 +18235,6 @@ 34: smi match: *C(C=O)C=O *C(C=O)C=O 34: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 34: smi match: O=CC=CC=O O=CC=CC=O - 31/208 Test #38: graphmolMemTest1 ....................... Passed 0.06 sec -test 39 - Start 39: resMolSupplierTest - -39: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest -39: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 34: smi match: O=CN(O)C=O O=CN(O)C=O 34: smi match: O=CN(S)C=O O=CN(S)C=O 34: smi match: O=CNC=O O=CNC=O @@ -18496,6 +18491,8 @@ 34: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 34: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O 34: smi match: *N(*)C*=O *N(*)C*=O +32: [07:09:17] Maximum BFS search size exceeded. +32: This is likely due to a highly symmetric fused ring system. 34: smi match: O=*C[OH] O=*C[OH] 34: smi match: *=C*=O *=C*=O 34: smi match: *=CC#N *=CC#N @@ -18516,8 +18513,6 @@ 34: smi match: N~N~N N~N~N 34: smi match: *N=N* *N=N* 34: smi match: *CC[OH] *CC[OH] -32: [20:16:54] Maximum BFS search size exceeded. -32: This is likely due to a highly symmetric fused ring system. 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] @@ -18592,105 +18587,151 @@ 34: smi match: * * 34: smi match: ***** ***** 34: smi match: NC(N)=O NC(N)=O -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing sf.net issue 280. -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing sf.net issue 285. -34: [20:16:54] done -34: [20:16:54] done -34: [20:16:54] done -34: [20:16:54] done -34: [20:16:54] done -34: [20:16:54] done -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing Github2441: Add RDProps interface to Conformers. -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing Issue2510: Pickle Confs as double. -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing loading pickled mols with conformers -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing conformer reading/writing options -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing property reading options -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing property reading options -34: [20:16:54] done -34: [20:16:54] ------------------------------------- -34: [20:16:54] Testing boost::serialization integration -34: [20:16:54] done - 32/208 Test #34: graphmoltestPickler .................... Passed 2.43 sec +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing sf.net issue 280. +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing sf.net issue 285. +34: [07:09:18] done +34: [07:09:18] done +34: [07:09:18] done +34: [07:09:18] done +34: [07:09:18] done +34: [07:09:18] done +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing Github2441: Add RDProps interface to Conformers. +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing Issue2510: Pickle Confs as double. +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing loading pickled mols with conformers +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing conformer reading/writing options +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing property reading options +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing property reading options +34: [07:09:18] done +34: [07:09:18] ------------------------------------- +34: [07:09:18] Testing boost::serialization integration +34: [07:09:18] done + 30/208 Test #34: graphmoltestPickler .................... Passed 0.57 sec +test 38 + Start 38: graphmolMemTest1 + +38: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 +38: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 + 31/208 Test #38: graphmolMemTest1 ....................... Passed 0.01 sec +test 39 + Start 39: resMolSupplierTest + +39: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest +39: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 +3: dynamic RDAny:0.58217 s +3: static RDValue:1e-06 s +3: dynamic RDValue:0.046628 s +3: deleted! +3: [07:09:18] ------------------------------------- +3: [07:09:18] Testing String Pickle Roundtrips. +3: [07:09:18] done +3: [07:09:18] ------------------------------------- +3: [07:09:18] Testing conversion of vect to string. +3: [07:09:18] done +3: [07:09:18] ------------------------------------- +3: [07:09:18] Testing returning const references. +3: [07:09:18] any cast +3: [07:09:18] done: 0.001827 300000 +3: [07:09:18] copy +3: [07:09:18] done: 0.001839 300000 +3: [07:09:18] ref +3: [07:09:18] done: 0.001824 300000 +3: [07:09:18] dict +3: [07:09:18] done: 0.007007 300000 +3: [07:09:18] ref with hasVal +3: [07:09:18] done: 0.002535 300000 +3: [07:09:18] done +3: [07:09:18] ------------------------------------- +3: [07:09:18] Testing dict update. +3: [07:09:18] done +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! +3: deleted! + 32/208 Test #3: testDict ............................... Passed 2.47 sec test 40 Start 40: molBundleTest 40: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest 40: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 40: Test timeout computed to be: 1500 - 33/208 Test #40: molBundleTest .......................... Passed 0.12 sec + 33/208 Test #40: molBundleTest .......................... Passed 0.04 sec test 41 Start 41: testSGroup 41: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup 41: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 41: Test timeout computed to be: 1500 - 34/208 Test #41: testSGroup ............................. Passed 0.25 sec + 34/208 Test #41: testSGroup ............................. Passed 0.05 sec test 42 Start 42: test-valgrind 42: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind 42: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 42: Test timeout computed to be: 1500 - 35/208 Test #42: test-valgrind .......................... Passed 0.15 sec + 35/208 Test #42: test-valgrind .......................... Passed 0.04 sec test 43 Start 43: graphmolTestsCatch 43: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch 43: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 43: Test timeout computed to be: 1500 -43: [20:16:55] WARNING: not removing hydrogen atom without neighbors -43: [20:16:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [20:16:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [20:16:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [20:16:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [20:16:55] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [20:16:55] Explicit valence for atom # 1 N, 6, is greater than permitted -43: [20:16:55] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [20:16:55] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [20:16:55] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [20:16:55] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [20:16:55] non-ring atom 2 marked aromatic -43: [20:16:55] non-ring atom 2 marked aromatic -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [20:16:55] Explicit valence for atom # 1 O, 3, is greater than permitted -43: [20:16:55] Explicit valence for atom # 4 F, 2, is greater than permitted -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 -43: [20:16:55] Explicit valence for atom # 1 C, 5, is greater than permitted -43: [20:16:55] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [20:16:55] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [20:16:55] WARNING: not removing hydrogen atom with wedged bond -43: [20:16:55] WARNING: not removing hydrogen atom without neighbors -43: [20:16:55] WARNING: not removing hydrogen atom without neighbors -43: [20:16:55] WARNING: not removing hydrogen atom without neighbors -43: [20:16:55] WARNING: not removing hydrogen atom without neighbors -43: [20:16:55] Unreasonable formal charge on hydrogen # 0. -43: [20:16:55] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [20:16:55] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [20:16:55] +43: [07:09:18] WARNING: not removing hydrogen atom without neighbors +43: [07:09:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [07:09:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [07:09:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [07:09:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [07:09:18] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [07:09:18] Explicit valence for atom # 1 N, 6, is greater than permitted +43: [07:09:18] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [07:09:18] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [07:09:18] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [07:09:18] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [07:09:18] non-ring atom 2 marked aromatic +43: [07:09:18] non-ring atom 2 marked aromatic +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [07:09:18] Explicit valence for atom # 1 O, 3, is greater than permitted +43: [07:09:18] Explicit valence for atom # 4 F, 2, is greater than permitted +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 6 7 8 +43: [07:09:18] Explicit valence for atom # 1 C, 5, is greater than permitted +43: [07:09:18] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [07:09:18] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [07:09:18] WARNING: not removing hydrogen atom with wedged bond +43: [07:09:18] WARNING: not removing hydrogen atom without neighbors +43: [07:09:18] WARNING: not removing hydrogen atom without neighbors +43: [07:09:18] WARNING: not removing hydrogen atom without neighbors +43: [07:09:18] WARNING: not removing hydrogen atom without neighbors +43: [07:09:18] Unreasonable formal charge on hydrogen # 0. +43: [07:09:18] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [07:09:18] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18699,7 +18740,7 @@ 43: Failed Expression: at 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18708,7 +18749,7 @@ 43: Failed Expression: at->hasOwningMol() 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18717,7 +18758,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18726,7 +18767,7 @@ 43: Failed Expression: at 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18735,7 +18776,7 @@ 43: Failed Expression: at->hasOwningMol() 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18744,7 +18785,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18753,7 +18794,7 @@ 43: Failed Expression: at 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18762,7 +18803,7 @@ 43: Failed Expression: at->hasOwningMol() 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18771,7 +18812,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18780,7 +18821,7 @@ 43: Failed Expression: atom_pin 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18789,7 +18830,7 @@ 43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18798,11 +18839,11 @@ 43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 43: **** 43: -43: [20:16:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [20:16:55] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [20:16:55] WARNING: not removing hydrogen atom without neighbors -43: [20:16:55] Explicit valence for atom # 1 F greater than permitted -43: [20:16:55] +43: [07:09:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [07:09:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [07:09:18] WARNING: not removing hydrogen atom without neighbors +43: [07:09:18] Explicit valence for atom # 1 F greater than permitted +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18811,7 +18852,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18820,7 +18861,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18829,7 +18870,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [20:16:55] +43: [07:09:18] 43: 43: **** 43: Pre-condition Violation @@ -18838,20 +18879,20 @@ 43: Failed Expression: 0 43: **** 43: -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [20:16:55] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [20:16:55] Unusual charge on atom 0 number of radical electrons set to zero -43: [20:16:55] Unusual charge on atom 0 number of radical electrons set to zero -43: [20:16:55] Unusual charge on atom 0 number of radical electrons set to zero -43: [20:16:55] non-ring atom 0 marked aromatic -43: [20:16:55] non-ring atom 0 marked aromatic +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [07:09:18] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [07:09:18] Unusual charge on atom 0 number of radical electrons set to zero +43: [07:09:18] Unusual charge on atom 0 number of radical electrons set to zero +43: [07:09:18] Unusual charge on atom 0 number of radical electrons set to zero +43: [07:09:18] non-ring atom 0 marked aromatic +43: [07:09:18] non-ring atom 0 marked aromatic 43: =============================================================================== 43: All tests passed (1316 assertions in 75 test cases) 43: - 36/208 Test #43: graphmolTestsCatch ..................... Passed 0.41 sec + 36/208 Test #43: graphmolTestsCatch ..................... Passed 0.09 sec test 44 Start 44: graphmolSGroupCatch @@ -18861,7 +18902,7 @@ 44: =============================================================================== 44: All tests passed (120 assertions in 6 test cases) 44: - 37/208 Test #44: graphmolSGroupCatch .................... Passed 0.12 sec + 37/208 Test #44: graphmolSGroupCatch .................... Passed 0.06 sec test 45 Start 45: graphmolAdjustQueryCatch @@ -18871,39 +18912,46 @@ 45: =============================================================================== 45: All tests passed (281 assertions in 10 test cases) 45: - 38/208 Test #45: graphmolAdjustQueryCatch ............... Passed 0.34 sec + 38/208 Test #45: graphmolAdjustQueryCatch ............... Passed 0.09 sec test 46 Start 46: chiralityTestsCatch 46: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch 46: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 -46: [20:16:56] unable to set wavy bonds for double bonds: 3 -46: [20:16:56] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [20:16:56] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [20:16:56] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [20:16:56] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [20:16:56] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [20:16:56] Warning: molecule is tagged as 3D, but all Z coords are zero -46: [20:16:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -46: [20:16:56] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -46: =============================================================================== -46: All tests passed (1587 assertions in 50 test cases) -46: - 39/208 Test #46: chiralityTestsCatch .................... Passed 0.44 sec -test 47 - Start 47: canonTestsCatch - -47: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch -47: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -32: [20:16:56] Maximum BFS search size exceeded. +32: [07:09:18] Maximum BFS search size exceeded. 32: This is likely due to a highly symmetric fused ring system. 32: F/C=C/Cl +46: [07:09:18] unable to set wavy bonds for double bonds: 3 32: [H]/C(F)=C(/[H])Cl 32: F/C=C/Cl 32: F/C=C/Cl 32: C/C(F)=C(/C)Cl +46: [07:09:18] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [07:09:18] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [07:09:18] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [07:09:18] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [07:09:18] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [07:09:18] Warning: molecule is tagged as 3D, but all Z coords are zero +46: [07:09:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +46: [07:09:18] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 39/208 Test #32: graphmolMolOpsTest ..................... Passed 1.75 sec +test 47 + Start 47: canonTestsCatch + +47: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch +47: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +46: =============================================================================== +46: All tests passed (1587 assertions in 50 test cases) +46: + 40/208 Test #46: chiralityTestsCatch .................... Passed 0.12 sec +test 48 + Start 48: moliteratorTestsCatch + +48: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch +48: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 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 @@ -18911,14 +18959,7 @@ 47: =============================================================================== 47: All tests passed (47 assertions in 2 test cases) 47: - 40/208 Test #47: canonTestsCatch ........................ Passed 0.13 sec -test 48 - Start 48: moliteratorTestsCatch - -48: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch -48: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 - 41/208 Test #32: graphmolMolOpsTest ..................... Passed 5.93 sec + 41/208 Test #47: canonTestsCatch ........................ Passed 0.03 sec test 49 Start 49: testDepictor @@ -18928,7 +18969,7 @@ 48: =============================================================================== 48: All tests passed (8 assertions in 3 test cases) 48: - 42/208 Test #48: moliteratorTestsCatch .................. Passed 0.13 sec + 42/208 Test #48: moliteratorTestsCatch .................. Passed 0.04 sec test 50 Start 50: depictorCatch @@ -18938,61 +18979,39 @@ 50: =============================================================================== 50: All tests passed (65 assertions in 4 test cases) 50: - 43/208 Test #50: depictorCatch .......................... Passed 0.17 sec + 43/208 Test #50: depictorCatch .......................... Passed 0.05 sec test 51 Start 51: pyDepictor 51: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" 51: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap 51: Test timeout computed to be: 1500 -49: [20:16:59] Warning: stereochemistry around double bond may be incorrect in depiction. - 44/208 Test #49: testDepictor ........................... Passed 2.52 sec +49: [07:09:19] Warning: stereochemistry around double bond may be incorrect in depiction. + 44/208 Test #49: testDepictor ........................... Passed 0.65 sec test 52 Start 52: smiTest1 52: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 52: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 52: Test timeout computed to be: 1500 -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] WARNING: not removing hydrogen atom without neighbors -52: [20:16:59] Invalid chiral specification on atom 0 -52: [20:16:59] Invalid chiral specification on atom 0 -52: [20:16:59] Invalid chiral specification on atom 0 -52: [20:16:59] Invalid chiral specification on atom 0 -52: [20:16:59] Invalid chiral specification on atom 0 -52: [20:17:00] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -52: [20:17:00] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -51: ....E..... -51: ====================================================================== -51: ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) -51: ---------------------------------------------------------------------- -51: Traceback (most recent call last): -51: File "/build/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D -51: dmat3D = getDistMat(mol) -51: ^^^^^^^^^^^^^^^ -51: File "/build/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 1.430s -51: -51: FAILED (errors=1) +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] WARNING: not removing hydrogen atom without neighbors +52: [07:09:19] Invalid chiral specification on atom 0 +52: [07:09:19] Invalid chiral specification on atom 0 +52: [07:09:19] Invalid chiral specification on atom 0 +52: [07:09:19] Invalid chiral specification on atom 0 +52: [07:09:19] Invalid chiral specification on atom 0 +52: [07:09:19] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +52: [07:09:19] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 52: --C1CCC2(CC1)CCCCC2CCC1CCCC1 52: smi: ClC1CCCCC1 52: smi: ClC1CCCCC1 @@ -19007,36 +19026,87 @@ 52: CbC(bC)aC 52: O.C 52: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -52: [20:17:01] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -52: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -52: [20:17:01] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -52: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -52: [20:17:01] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -52: [20:17:01] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -52: [20:17:01] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [20:17:01] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [20:17:01] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [20:17:01] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [20:17:01] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -52: [20:17:01] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -52: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [07:09:19] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +52: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +52: [07:09:19] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +52: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +52: [07:09:19] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +52: [07:09:19] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +52: [07:09:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [07:09:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [07:09:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [07:09:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [07:09:19] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +52: [07:09:19] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +52: [07:09:19] 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: [20:17:01] SMILES Parse Error: extra close parentheses while parsing: C) -52: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 45/208 Test #52: smiTest1 ............................... Passed 2.21 sec +52: [07:09:19] SMILES Parse Error: extra close parentheses while parsing: C) +52: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 45/208 Test #52: smiTest1 ............................... Passed 0.45 sec test 53 Start 53: smiTest2 53: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 53: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 53: Test timeout computed to be: 1500 - 46/208 Test #51: pyDepictor .............................***Failed 4.52 sec +53: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +53: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +53: [07:09:19] SMILES Parse Error: syntax error while parsing: - +53: [07:09:19] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +53: [07:09:19] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +53: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +53: [07:09:19] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +53: [07:09:19] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +53: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +53: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +53: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +53: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +53: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +53: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +53: [07:09:19] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 46/208 Test #53: smiTest2 ............................... Passed 0.02 sec +test 54 + Start 54: cxsmilesTest + +54: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest +54: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse +54: Test timeout computed to be: 1500 + 47/208 Test #54: cxsmilesTest ........................... Passed 0.04 sec +test 55 + Start 55: smaTest1 + +55: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 +55: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse +55: Test timeout computed to be: 1500 +51: ....E..... +51: ====================================================================== +51: ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) +51: ---------------------------------------------------------------------- +51: Traceback (most recent call last): +51: File "/build/rdkit-202209.3/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 188, in test5SamplingMimic3D +51: dmat3D = getDistMat(mol) +51: ^^^^^^^^^^^^^^^ +51: File "/build/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 0.436s +51: +51: FAILED (errors=1) + 48/208 Test #51: pyDepictor .............................***Failed 1.25 sec ....E..... ====================================================================== ERROR: test5SamplingMimic3D (__main__.TestCase.test5SamplingMimic3D) @@ -19056,119 +19126,76 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 10 tests in 1.430s +Ran 10 tests in 0.436s FAILED (errors=1) -test 54 - Start 54: cxsmilesTest - -54: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest -54: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse -54: Test timeout computed to be: 1500 -53: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -53: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -53: [20:17:01] SMILES Parse Error: syntax error while parsing: - -53: [20:17:01] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -53: [20:17:01] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -53: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -53: [20:17:01] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -53: [20:17:01] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -53: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -53: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -53: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -53: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -53: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -53: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -53: [20:17:01] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 47/208 Test #53: smiTest2 ............................... Passed 0.07 sec -test 55 - Start 55: smaTest1 - -55: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 -55: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse -55: Test timeout computed to be: 1500 - 48/208 Test #54: cxsmilesTest ........................... Passed 0.18 sec test 56 Start 56: smiTestCatch 56: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 56: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 56: Test timeout computed to be: 1500 -56: [20:17:02] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -56: [20:17:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -56: [20:17:02] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -56: [20:17:02] SMARTS Parse Error: unclosed ring for input: 'C1C' -56: [20:17:02] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -56: [20:17:02] SMARTS Parse Error: syntax error while parsing: C)foo -56: [20:17:02] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -56: [20:17:02] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -56: [20:17:02] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -56: [20:17:02] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -55: [20:17:02] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -55: [20:17:02] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -55: [20:17:02] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -55: [20:17:02] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -55: [20:17:02] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -55: [20:17:02] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -56: [20:17:02] w block attempts to set wedging on bond 0 more than once. -56: [20:17:02] improperly formatted w block -56: [20:17:02] atom 3 is not associated with bond 1 in w block -56: =============================================================================== -56: All tests passed (969 assertions in 49 test cases) -56: - 49/208 Test #56: smiTestCatch ........................... Passed 1.12 sec +56: [07:09:20] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +56: [07:09:20] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +56: [07:09:20] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +56: [07:09:20] SMARTS Parse Error: unclosed ring for input: 'C1C' +56: [07:09:20] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +56: [07:09:20] SMARTS Parse Error: syntax error while parsing: C)foo +56: [07:09:20] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +56: [07:09:20] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +56: [07:09:20] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +56: [07:09:20] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +55: [07:09:20] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +55: [07:09:20] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +55: [07:09:20] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +55: [07:09:20] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +55: [07:09:20] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +55: [07:09:20] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 49/208 Test #55: smaTest1 ............................... Passed 0.29 sec test 57 Start 57: nontetrahedralCatch 57: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 57: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 - 50/208 Test #55: smaTest1 ............................... Passed 1.29 sec +57: [07:09:20] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [07:09:20] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [07:09:20] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [07:09:20] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [07:09:20] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [07:09:20] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [07:09:20] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +57: [07:09:20] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +56: [07:09:20] w block attempts to set wedging on bond 0 more than once. +56: [07:09:20] improperly formatted w block +57: [07:09:20] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +56: [07:09:20] atom 3 is not associated with bond 1 in w block +56: =============================================================================== +56: All tests passed (969 assertions in 49 test cases) +56: +57: =============================================================================== +57: All tests passed (308 assertions in 9 test cases) +57: + 50/208 Test #57: nontetrahedralCatch .................... Passed 0.09 sec test 58 Start 58: fileParsersTest1 58: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 58: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 58: Test timeout computed to be: 1500 -57: [20:17:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: *************************************** -58: *************************************** -57: [20:17:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [20:17:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [20:17:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [20:17:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [20:17:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [20:17:03] bond with order 0 found on line 7. This is not part of the MDL specification. -58: [20:17:03] unrecognized query bond type, 9, found on line 7. Using an "any" query. -57: [20:17:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [20:17:03] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [20:17:03] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -57: =============================================================================== -57: All tests passed (308 assertions in 9 test cases) -57: - 51/208 Test #57: nontetrahedralCatch .................... Passed 0.37 sec + 51/208 Test #56: smiTestCatch ........................... Passed 0.23 sec test 59 Start 59: testMolSupplier 59: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier 59: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 59: Test timeout computed to be: 1500 -58: [20:17:03] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -58: [20:17:03] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -58: [20:17:03] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:03] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:03] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:03] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:03] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:03] Warning: molecule is tagged as 3D, but all Z coords are zero -59: [20:17:03] +59: [07:09:20] 59: ----------------------------------------- -58: generating smiles -58: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -58: converting back -58: check isomorphism -59: [20:17:03] +58: *************************************** +58: *************************************** +59: [07:09:20] 59: 59: **** 59: Invariant Violation @@ -19177,220 +19204,233 @@ 59: Failed Expression: nSwaps < 2 59: **** 59: -59: [20:17:04] Finished: testMolSup() -59: [20:17:04] ----------------------------------------- +58: [07:09:20] bond with order 0 found on line 7. This is not part of the MDL specification. +58: [07:09:20] unrecognized query bond type, 9, found on line 7. Using an "any" query. +58: [07:09:20] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +58: [07:09:20] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +58: [07:09:20] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:20] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:20] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:20] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:20] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:20] Warning: molecule is tagged as 3D, but all Z coords are zero +58: generating smiles +58: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +58: converting back +58: check isomorphism +59: [07:09:20] Finished: testMolSup() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testRandMolSup() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testRandMolSup() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testSmilesSup() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testSmilesSup() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] ------------------------------------------------------ -59: [20:17:04] SMILES Parse Error: syntax error while parsing: fail -59: [20:17:04] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -59: [20:17:04] ERROR: Smiles parse error on line 3 -59: [20:17:04] ERROR: Cannot create molecule from : 'fail' -59: [20:17:04] ------------------------------------------------------ -59: [20:17:04] ------------------------------------------------------ -59: [20:17:04] >>> This may result in an infinite loop. It should finish almost immediately: -59: [20:17:04] <<< done. -59: [20:17:04] Finished: testSmilesSupFromText() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] ------------------------------------------------------ +59: [07:09:20] SMILES Parse Error: syntax error while parsing: fail +59: [07:09:20] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +59: [07:09:20] ERROR: Smiles parse error on line 3 +59: [07:09:20] ERROR: Cannot create molecule from : 'fail' +59: [07:09:20] ------------------------------------------------------ +59: [07:09:20] ------------------------------------------------------ +59: [07:09:20] >>> This may result in an infinite loop. It should finish almost immediately: +59: [07:09:20] <<< done. +59: [07:09:20] Finished: testSmilesSupFromText() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testSmilesWriter() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testSmilesWriter() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testSDWriter() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testSDWriter() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testSDSupplierEnding() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testSDSupplierEnding() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testSuppliersEmptyFile() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testSuppliersEmptyFile() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testCisTrans() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testCisTrans() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testStereoRound() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testStereoRound() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testIssue226() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testIssue226() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:04] Finished: testTDTSupplier1() -59: [20:17:04] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testTDTSupplier1() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:04] ----------------------------------------- -59: [20:17:05] Finished: testTDTSupplier2() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testTDTSupplier2() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testTDTSupplier3() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testTDTSupplier3() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testSDSupplierFromText() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testSDSupplierFromText() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] ERROR: Problems encountered parsing data fields -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] ERROR: Problems encountered parsing data fields -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Spurious data before the first property will be ignored -59: [20:17:05] Property will be truncated after the first blank line -59: [20:17:05] Property will be truncated after the first blank line -59: [20:17:05] Property will be truncated after the first blank line -59: [20:17:05] Finished: testSDSupplierStrLax1() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] ERROR: Problems encountered parsing data fields +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] ERROR: Problems encountered parsing data fields +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Spurious data before the first property will be ignored +59: [07:09:20] Property will be truncated after the first blank line +59: [07:09:20] Property will be truncated after the first blank line +59: [07:09:20] Property will be truncated after the first blank line +59: [07:09:20] Finished: testSDSupplierStrLax1() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] ERROR: Problems encountered parsing data fields -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Property will be truncated after the first blank line -59: [20:17:05] Finished: testSDSupplierStrLax2() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] ERROR: Problems encountered parsing data fields +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Property will be truncated after the first blank line +59: [07:09:20] Finished: testSDSupplierStrLax2() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] ERROR: Problems encountered parsing data fields -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] ERROR: Problems encountered parsing data fields -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Spurious data before the first property will be ignored -59: [20:17:05] Property will be truncated after the first blank line -59: [20:17:05] Property will be truncated after the first blank line -59: [20:17:05] Property will be truncated after the first blank line -59: [20:17:05] Finished: testSDSupplierFromTextStrLax1() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] ERROR: Problems encountered parsing data fields +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] ERROR: Problems encountered parsing data fields +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Spurious data before the first property will be ignored +59: [07:09:20] Property will be truncated after the first blank line +59: [07:09:20] Property will be truncated after the first blank line +59: [07:09:20] Property will be truncated after the first blank line +59: [07:09:20] Finished: testSDSupplierFromTextStrLax1() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] ERROR: Problems encountered parsing data fields -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Property will be truncated after the first blank line -59: [20:17:05] Finished: testSDSupplierFromTextStrLax2() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] ERROR: Problems encountered parsing data fields +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Property will be truncated after the first blank line +59: [07:09:20] Finished: testSDSupplierFromTextStrLax2() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testIssue265() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testIssue265() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] ERROR: End of data field name not found -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Explicit valence for atom # 0 F, 2, is greater than permitted -59: [20:17:05] ERROR: Could not sanitize molecule ending on line 16 -59: [20:17:05] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -59: [20:17:05] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] ERROR: Bond line too short: 'M END' on line 18 -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Finished: testSDErrorHandling() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] ERROR: End of data field name not found +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Explicit valence for atom # 0 F, 2, is greater than permitted +59: [07:09:20] ERROR: Could not sanitize molecule ending on line 16 +59: [07:09:20] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +59: [07:09:20] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] ERROR: Bond line too short: 'M END' on line 18 +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Finished: testSDErrorHandling() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testIssue381() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testIssue381() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testSetStreamIndices() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testSetStreamIndices() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testMixIterAndRandom() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testMixIterAndRandom() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- 59: build: -59: [20:17:05] Finished: testRemoveHs() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] Finished: testRemoveHs() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testGetItemText() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testGetItemText() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testForwardSDSupplier() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testForwardSDSupplier() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testMissingCRSDSupplier() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testMissingCRSDSupplier() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testIssue3482695() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testIssue3482695() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] ERROR: Cannot convert 'foo' to unsigned int on line 557 -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Finished: testIssue3525673() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] ERROR: Cannot convert 'foo' to unsigned int on line 557 +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Finished: testIssue3525673() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testBlankLinesInProps() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testBlankLinesInProps() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testSkipLines() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testSkipLines() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testGitHub23() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testGitHub23() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testGitHub88() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testGitHub88() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -25: Checking against /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -59: [20:17:05] Finished: testGitHub2285() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testGitHub2285() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -59: [20:17:05] ERROR: Smiles parse error on line 1 -59: [20:17:05] ERROR: Cannot create molecule from : 'c1ccccc' -59: [20:17:05] SMILES Parse Error: extra open parentheses for input: 'C(C' -59: [20:17:05] ERROR: Smiles parse error on line 3 -59: [20:17:05] ERROR: Cannot create molecule from : 'C(C' -59: [20:17:05] Explicit valence for atom # 1 C, 5, is greater than permitted -59: [20:17:05] ERROR: Could not sanitize molecule on line 5 -59: [20:17:05] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -59: [20:17:05] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [20:17:05] ERROR: Could not sanitize molecule ending on line 21 -59: [20:17:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [20:17:05] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [20:17:05] ERROR: Could not sanitize molecule ending on line 21 -59: [20:17:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [20:17:05] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [20:17:05] ERROR: Could not sanitize molecule ending on line 21 -59: [20:17:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [20:17:05] ERROR: Atom line too short: ' -9.6' on line 28 -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Explicit valence for atom # 1 F, 2, is greater than permitted -59: [20:17:05] ERROR: Could not sanitize molecule ending on line 21 -59: [20:17:05] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -59: [20:17:05] ERROR: Atom line too short: ' -9.6' on line 28 -59: [20:17:05] ERROR: moving to the beginning of the next molecule -59: [20:17:05] Finished: testGitHub2479() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +59: [07:09:20] ERROR: Smiles parse error on line 1 +59: [07:09:20] ERROR: Cannot create molecule from : 'c1ccccc' +59: [07:09:20] SMILES Parse Error: extra open parentheses for input: 'C(C' +59: [07:09:20] ERROR: Smiles parse error on line 3 +59: [07:09:20] ERROR: Cannot create molecule from : 'C(C' +59: [07:09:20] Explicit valence for atom # 1 C, 5, is greater than permitted +59: [07:09:20] ERROR: Could not sanitize molecule on line 5 +59: [07:09:20] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +59: [07:09:20] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [07:09:20] ERROR: Could not sanitize molecule ending on line 21 +59: [07:09:20] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [07:09:20] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [07:09:20] ERROR: Could not sanitize molecule ending on line 21 +59: [07:09:20] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [07:09:20] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [07:09:20] ERROR: Could not sanitize molecule ending on line 21 +59: [07:09:20] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [07:09:20] ERROR: Atom line too short: ' -9.6' on line 28 +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Explicit valence for atom # 1 F, 2, is greater than permitted +59: [07:09:20] ERROR: Could not sanitize molecule ending on line 21 +59: [07:09:20] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +59: [07:09:20] ERROR: Atom line too short: ' -9.6' on line 28 +59: [07:09:20] ERROR: moving to the beginning of the next molecule +59: [07:09:20] Finished: testGitHub2479() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] +59: [07:09:20] ----------------------------------------- +59: [07:09:20] 59: 59: **** 59: Invariant Violation @@ -19399,76 +19439,72 @@ 59: Failed Expression: bnd 59: **** 59: -59: [20:17:05] Finished: testGitHub2881() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] Finished: testGitHub2881() +59: [07:09:20] ----------------------------------------- 59: -59: [20:17:05] ----------------------------------------- -59: [20:17:05] Finished: testGitHub3517() -59: [20:17:05] ----------------------------------------- +59: [07:09:20] ----------------------------------------- +59: [07:09:20] Finished: testGitHub3517() +59: [07:09:20] ----------------------------------------- 59: - 52/208 Test #59: testMolSupplier ........................ Passed 2.05 sec + 52/208 Test #59: testMolSupplier ........................ Passed 0.48 sec test 60 Start 60: testGeneralFileReader 60: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader 60: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 60: Test timeout computed to be: 1500 -60: [20:17:05] +60: [07:09:20] 60: ----------------------------------------- -60: [20:17:05] Finished: testDetermineFormat() -60: [20:17:05] ----------------------------------------- +60: [07:09:20] Finished: testDetermineFormat() +60: [07:09:20] ----------------------------------------- 60: -60: [20:17:05] +60: [07:09:20] 60: ----------------------------------------- -60: [20:17:05] Finished: testSdf() -60: [20:17:05] ----------------------------------------- +60: [07:09:20] Finished: testSdf() +60: [07:09:20] ----------------------------------------- 60: -60: [20:17:05] +60: [07:09:20] 60: ----------------------------------------- -60: [20:17:05] Finished: testSmi() -60: [20:17:05] ----------------------------------------- +60: [07:09:20] Finished: testSmi() +60: [07:09:20] ----------------------------------------- 60: -60: [20:17:05] +60: [07:09:20] 60: ----------------------------------------- -25: All 191 tests passed -60: [20:17:06] Finished: testMae() -60: [20:17:06] ----------------------------------------- +60: [07:09:20] Finished: testMae() +60: [07:09:20] ----------------------------------------- 60: -60: [20:17:06] +60: [07:09:20] 60: ----------------------------------------- -60: [20:17:06] Finished: testTdt() -60: [20:17:06] ----------------------------------------- +60: [07:09:20] Finished: testTdt() +60: [07:09:20] ----------------------------------------- 60: - 53/208 Test #60: testGeneralFileReader .................. Passed 0.88 sec + 53/208 Test #60: testGeneralFileReader .................. Passed 0.22 sec test 61 Start 61: testMultithreadedMolSupplier 61: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 61: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 61: Test timeout computed to be: 1500 +61: [07:09:21] +61: ----------------------------------------- +25: Checking against /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed 25: 25: Computing MMFF94 energies for /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -61: [20:17:06] -61: ----------------------------------------- - 54/208 Test #37: hanoiTest .............................. Passed 15.05 sec + 54/208 Test #37: hanoiTest .............................. Passed 4.20 sec test 62 Start 62: testMolWriter 62: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 62: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 62: Test timeout computed to be: 1500 -62: [20:17:11] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [20:17:11] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [20:17:11] Warning: molecule is tagged as 3D, but all Z coords are zero -62: [20:17:11] bond with order 0 found on line 11. This is not part of the MDL specification. -62: [20:17:11] bond with order 0 found on line 16. This is not part of the MDL specification. -58: [20:17:11] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [20:17:11] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [20:17:11] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [20:17:11] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [20:17:11] deprecated group abbreviation ignored on line 24 +58: [07:09:22] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [07:09:22] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [07:09:22] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [07:09:22] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [07:09:22] 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: [20:17:11] +58: [07:09:22] 58: 58: **** 58: Post-condition Violation @@ -19477,21 +19513,26 @@ 58: Failed Expression: anum > -1 58: **** 58: - 55/208 Test #62: testMolWriter .......................... Passed 3.00 sec +62: [07:09:22] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [07:09:22] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [07:09:22] Warning: molecule is tagged as 3D, but all Z coords are zero +62: [07:09:22] bond with order 0 found on line 11. This is not part of the MDL specification. +62: [07:09:22] bond with order 0 found on line 16. This is not part of the MDL specification. + 55/208 Test #62: testMolWriter .......................... Passed 0.48 sec test 63 Start 63: testTplParser 63: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 63: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 63: Test timeout computed to be: 1500 - 56/208 Test #63: testTplParser .......................... Passed 0.29 sec + 56/208 Test #63: testTplParser .......................... Passed 0.05 sec test 64 Start 64: testMol2ToMol 64: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 64: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 64: Test timeout computed to be: 1500 - 57/208 Test #64: testMol2ToMol .......................... Passed 0.39 sec + 57/208 Test #64: testMol2ToMol .......................... Passed 0.06 sec test 65 Start 65: testSequence @@ -20482,39 +20523,39 @@ 65: CONECT 27 28 28 29 65: END 65: - 58/208 Test #65: testSequence ........................... Passed 0.38 sec + 58/208 Test #65: testSequence ........................... Passed 0.08 sec test 66 Start 66: testExtendedStereoParsing 66: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing 66: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 66: Test timeout computed to be: 1500 - 59/208 Test #66: testExtendedStereoParsing .............. Passed 0.08 sec + 59/208 Test #66: testExtendedStereoParsing .............. Passed 0.05 sec test 67 Start 67: fileParsersCatchTest 67: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest 67: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 -67: [20:17:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -67: [20:17:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -67: [20:17:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [20:17:12] SGroup 1 is invalid and will be ignored -67: [20:17:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -67: [20:17:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [20:17:12] SGroup 1 is invalid and will be ignored -67: [20:17:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -67: [20:17:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -67: [20:17:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -67: [20:17:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -67: [20:17:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [20:17:12] SGroup 1 is invalid and will be ignored -67: [20:17:12] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -67: [20:17:12] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -67: [20:17:12] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -67: [20:17:12] SGroup 1 is invalid and will be ignored -67: [20:17:12] SGroup 3 referenced on line 40 not found. -67: [20:17:12] +67: [07:09:22] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +67: [07:09:22] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +67: [07:09:22] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [07:09:22] SGroup 1 is invalid and will be ignored +67: [07:09:22] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +67: [07:09:22] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [07:09:22] SGroup 1 is invalid and will be ignored +67: [07:09:22] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +67: [07:09:22] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +67: [07:09:22] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +67: [07:09:22] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +67: [07:09:22] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [07:09:22] SGroup 1 is invalid and will be ignored +67: [07:09:22] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +67: [07:09:22] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +67: [07:09:22] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +67: [07:09:22] SGroup 1 is invalid and will be ignored +67: [07:09:22] SGroup 3 referenced on line 40 not found. +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20523,8 +20564,8 @@ 67: Failed Expression: !d_bonds.empty() 67: **** 67: -67: [20:17:12] SGroup 3 referenced on line 40 not found. -67: [20:17:12] +67: [07:09:22] SGroup 3 referenced on line 40 not found. +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20533,13 +20574,13 @@ 67: Failed Expression: !d_bonds.empty() 67: **** 67: -67: [20:17:12] no bonds -67: [20:17:12] SGroup 1 is invalid and will be ignored -67: [20:17:12] SGroup line too short: 'M SBV 1 6' on line 42 -67: [20:17:12] SGroup 1 is invalid and will be ignored -67: [20:17:12] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -67: [20:17:12] SGroup 2 is invalid and will be ignored -67: [20:17:12] +67: [07:09:22] no bonds +67: [07:09:22] SGroup 1 is invalid and will be ignored +67: [07:09:22] SGroup line too short: 'M SBV 1 6' on line 42 +67: [07:09:22] SGroup 1 is invalid and will be ignored +67: [07:09:22] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +67: [07:09:22] SGroup 2 is invalid and will be ignored +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20548,7 +20589,7 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20557,8 +20598,8 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] multiple bonds with same bookmark -67: [20:17:12] +67: [07:09:22] multiple bonds with same bookmark +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20567,9 +20608,9 @@ 67: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 67: **** 67: -67: [20:17:12] bond is not part of the SubstanceGroup -67: [20:17:12] SGroup 2 is invalid and will be ignored -67: [20:17:12] +67: [07:09:22] bond is not part of the SubstanceGroup +67: [07:09:22] SGroup 2 is invalid and will be ignored +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20578,7 +20619,7 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20587,11 +20628,11 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] multiple atoms with same bookmark -67: [20:17:12] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -67: [20:17:12] SGroup 2 is invalid and will be ignored -67: [20:17:12] WARNING: final character of V3000 array is not ')' -67: [20:17:12] +67: [07:09:22] multiple atoms with same bookmark +67: [07:09:22] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +67: [07:09:22] SGroup 2 is invalid and will be ignored +67: [07:09:22] WARNING: final character of V3000 array is not ')' +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20600,8 +20641,8 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] WARNING: final character of V3000 array is not ')' -67: [20:17:12] +67: [07:09:22] WARNING: final character of V3000 array is not ')' +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20610,10 +20651,10 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] multiple bonds with same bookmark -67: [20:17:12] SGroup 1 is invalid and will be ignored -67: [20:17:12] WARNING: final character of V3000 array is not ')' -67: [20:17:12] +67: [07:09:22] multiple bonds with same bookmark +67: [07:09:22] SGroup 1 is invalid and will be ignored +67: [07:09:22] WARNING: final character of V3000 array is not ')' +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20622,8 +20663,8 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] WARNING: final character of V3000 array is not ')' -67: [20:17:12] +67: [07:09:22] WARNING: final character of V3000 array is not ')' +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20632,9 +20673,9 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] multiple atoms with same bookmark -67: [20:17:12] SGroup 1 is invalid and will be ignored -67: [20:17:12] +67: [07:09:22] multiple atoms with same bookmark +67: [07:09:22] SGroup 1 is invalid and will be ignored +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20643,7 +20684,7 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20652,9 +20693,9 @@ 67: Failed Expression: d_bondBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] multiple bonds with same bookmark -67: [20:17:12] SGroup 2 is invalid and will be ignored -67: [20:17:12] +67: [07:09:22] multiple bonds with same bookmark +67: [07:09:22] SGroup 2 is invalid and will be ignored +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20663,7 +20704,7 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20672,14 +20713,14 @@ 67: Failed Expression: d_atomBookmarks.count(mark) == 1 67: **** 67: -67: [20:17:12] multiple atoms with same bookmark -67: [20:17:12] SGroup 2 is invalid and will be ignored -67: [20:17:13] Explicit valence for atom # 2 O, 3, is greater than permitted -67: [20:17:13] Explicit valence for atom # 1 O, 3, is greater than permitted -67: [20:17:13] Explicit valence for atom # 1 C, 5, is greater than permitted -67: [20:17:13] sanitise [20:17:13] UNK: [20:17:13] Warning: molecule is tagged as 3D, but all Z coords are zero -67: [20:17:13] skipping block at line 7: 'BEGIN ATOM' -67: [20:17:13] +67: [07:09:22] multiple atoms with same bookmark +67: [07:09:22] SGroup 2 is invalid and will be ignored +67: [07:09:22] Explicit valence for atom # 2 O, 3, is greater than permitted +67: [07:09:22] Explicit valence for atom # 1 O, 3, is greater than permitted +67: [07:09:22] Explicit valence for atom # 1 C, 5, is greater than permitted +67: [07:09:22] sanitise [07:09:22] UNK: [07:09:22] Warning: molecule is tagged as 3D, but all Z coords are zero +67: [07:09:22] skipping block at line 7: 'BEGIN ATOM' +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20688,7 +20729,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [20:17:13] +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20697,7 +20738,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [20:17:13] +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20706,7 +20747,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [20:17:13] +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20715,7 +20756,7 @@ 67: Failed Expression: dp_inStream 67: **** 67: -67: [20:17:13] +67: [07:09:22] 67: 67: **** 67: Pre-condition Violation @@ -20724,9 +20765,9 @@ 67: Failed Expression: dp_sInStream != nullptr 67: **** 67: -67: [20:17:13] Found a SCD/SED line with missing/empty SDT specification at line 21 -67: [20:17:13] Found a SCD/SED line with missing/empty SDT specification at line 20 -67: [20:17:13] +67: [07:09:22] Found a SCD/SED line with missing/empty SDT specification at line 21 +67: [07:09:22] Found a SCD/SED line with missing/empty SDT specification at line 20 +67: [07:09:22] 67: 67: **** 67: Post-condition Violation @@ -20735,13 +20776,13 @@ 67: Failed Expression: anum > -1 67: **** 67: -67: [20:17:13] BEGIN SGROUP line not found on line 14 -67: [20:17:13] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -67: [20:17:13] END SGROUP line not found on line 14 -67: [20:17:13] END SGROUP line not found on line 14 -67: [20:17:13] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -67: [20:17:13] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -67: [20:17:13] +67: [07:09:22] BEGIN SGROUP line not found on line 14 +67: [07:09:22] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +67: [07:09:22] END SGROUP line not found on line 14 +67: [07:09:22] END SGROUP line not found on line 14 +67: [07:09:22] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +67: [07:09:22] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +67: [07:09:22] 67: 67: **** 67: Range Error @@ -20750,21 +20791,21 @@ 67: Failed Expression: 99 < 9 67: **** 67: -67: [20:17:13] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -67: [20:17:13] Multiple ATTCHPT values for atom 2 on line 9 -67: [20:17:13] Found a SCD/SED line with missing/empty SDT specification at line 12 -67: [20:17:13] SMARTS Parse Error: syntax error while parsing: [#6;R -67: [20:17:13] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -67: [20:17:13] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -67: [20:17:13] Skipping empty SMARTS value for SMARTSQ. -67: [20:17:13] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -67: [20:17:13] Found a SCD/SED line with missing/empty SDT specification at line 12 -67: [20:17:13] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -67: [20:17:13] Warning: molecule is tagged as 3D, but all Z coords are zero +67: [07:09:22] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +67: [07:09:22] Multiple ATTCHPT values for atom 2 on line 9 +67: [07:09:22] Found a SCD/SED line with missing/empty SDT specification at line 12 +67: [07:09:22] SMARTS Parse Error: syntax error while parsing: [#6;R +67: [07:09:22] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +67: [07:09:22] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +67: [07:09:22] Skipping empty SMARTS value for SMARTSQ. +67: [07:09:22] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +67: [07:09:22] Found a SCD/SED line with missing/empty SDT specification at line 12 +67: [07:09:22] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +67: [07:09:22] Warning: molecule is tagged as 3D, but all Z coords are zero 67: =============================================================================== 67: All tests passed (778 assertions in 67 test cases) 67: - 60/208 Test #67: fileParsersCatchTest ................... Passed 0.32 sec + 60/208 Test #67: fileParsersCatchTest ................... Passed 0.17 sec test 68 Start 68: testPropertyLists @@ -20774,7 +20815,7 @@ 68: =============================================================================== 68: All tests passed (94 assertions in 4 test cases) 68: - 61/208 Test #68: testPropertyLists ...................... Passed 0.12 sec + 61/208 Test #68: testPropertyLists ...................... Passed 0.05 sec test 69 Start 69: XYZFileParserCatchTest @@ -20784,51 +20825,49 @@ 69: =============================================================================== 69: All tests passed (100 assertions in 2 test cases) 69: - 62/208 Test #69: XYZFileParserCatchTest ................. Passed 0.14 sec + 62/208 Test #69: XYZFileParserCatchTest ................. Passed 0.05 sec test 70 Start 70: cdxmlParserCatchTest 70: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest 70: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 -70: [20:17:13] Invalid or missing fragment id from CDXML fragment, assigning new one... -70: [20:17:13] Explicit valence for atom # 3 N, 4, is greater than permitted -70: [20:17:13] CDXMLParser: failed sanitizing skipping fragment 32 -70: [20:17:13] Bad bond in CDXML skipping fragment 58... -70: [20:17:13] Invalid or missing fragment id from CDXML fragment, assigning new one... -70: [20:17:13] Bad bond in CDXML skipping fragment 58... -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] WARNING: not removing hydrogen atom without neighbors -70: [20:17:14] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. -70: [20:17:14] Incomplete atom labelling, cannot make bond -70: [20:17:14] Incomplete atom labelling, cannot make bond -70: [20:17:14] Incomplete atom labelling, cannot make bond -70: [20:17:14] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [20:17:14] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [20:17:14] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -70: [20:17:14] Failed to parse XML fragment 5 node: b attribute: Order: 5 -70: [20:17:14] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [20:17:14] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -70: [20:17:14] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -70: [20:17:14] Failed to parse XML fragment 5 node: b attribute: Order: 5 -70: =============================================================================== -70: All tests passed (200 assertions in 1 test case) -70: - 63/208 Test #70: cdxmlParserCatchTest ................... Passed 1.17 sec +70: [07:09:23] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [07:09:23] Explicit valence for atom # 3 N, 4, is greater than permitted +70: [07:09:23] CDXMLParser: failed sanitizing skipping fragment 32 +70: [07:09:23] Bad bond in CDXML skipping fragment 58... +70: [07:09:23] Invalid or missing fragment id from CDXML fragment, assigning new one... +70: [07:09:23] Bad bond in CDXML skipping fragment 58... +11: .................. +11: ---------------------------------------------------------------------- +11: Ran 18 tests in 6.811s +11: +11: OK +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] WARNING: not removing hydrogen atom without neighbors +70: [07:09:23] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. +70: [07:09:23] Incomplete atom labelling, cannot make bond +70: [07:09:23] Incomplete atom labelling, cannot make bond + 63/208 Test #11: pyBV ................................... Passed 7.37 sec test 71 Start 71: testSubstructMatch 71: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 71: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 71: Test timeout computed to be: 1500 +70: [07:09:23] Incomplete atom labelling, cannot make bond +70: [07:09:23] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [07:09:23] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [07:09:23] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +70: [07:09:23] Failed to parse XML fragment 5 node: b attribute: Order: 5 71: ----------------- Test 1 71: Done 71: @@ -20853,20 +20892,29 @@ 71: ----------------- Testing serial numbers on recursive queries 71: Done 71: -71: [20:17:14] ------------------------------------- -71: [20:17:14] Test multithreading +71: [07:09:23] ------------------------------------- +71: [07:09:23] Test multithreading 71: reading molecules +70: [07:09:23] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [07:09:23] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +70: [07:09:23] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +70: [07:09:23] 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 0.26 sec +test 72 + Start 72: substructTestCatch + +72: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +72: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct +72: Test timeout computed to be: 1500 71: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 71: processing 71: launch :0 71: launch :1 71: launch :2 71: launch :3 -11: .................. -11: ---------------------------------------------------------------------- -11: Ran 18 tests in 27.302s -11: -11: OK 71: done 71: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 71: processing2 @@ -20882,42 +20930,35 @@ 71: launch3 :1 71: launch3 :2 71: launch3 :3 - 64/208 Test #11: pyBV ................................... Passed 29.92 sec -test 72 - Start 72: substructTestCatch - -72: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -72: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct -72: Test timeout computed to be: 1500 71: done -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Test GitHub issue 15 -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Test GitHub issue 409 -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Test chiral matching -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Test dative-bond matching -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Test cis/trans matching -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Test cis/trans matching part 2 -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -71: [20:17:16] done -71: [20:17:16] ------------------------------------- -71: [20:17:16] Testing matching E/Z against Cis/Trans stereo bonds -71: [20:17:16] +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Test GitHub issue 15 +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Test GitHub issue 409 +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Test chiral matching +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Test dative-bond matching +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Test cis/trans matching +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Test cis/trans matching part 2 +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +71: [07:09:23] done +71: [07:09:23] ------------------------------------- +71: [07:09:23] Testing matching E/Z against Cis/Trans stereo bonds +71: [07:09:23] 71: 71: **** 71: Pre-condition Violation @@ -20926,7 +20967,7 @@ 71: Failed Expression: !matches.empty() 71: **** 71: -71: [20:17:16] +71: [07:09:23] 71: 71: **** 71: Pre-condition Violation @@ -20935,262 +20976,258 @@ 71: Failed Expression: !matches.empty() 71: **** 71: - 65/208 Test #71: testSubstructMatch ..................... Passed 2.34 sec + 65/208 Test #71: testSubstructMatch ..................... Passed 0.61 sec test 73 Start 73: testGenericGroups 73: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups 73: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups 73: Test timeout computed to be: 1500 -73: =============================================================================== -73: All tests passed (490 assertions in 18 test cases) -73: - 66/208 Test #73: testGenericGroups ...................... Passed 0.37 sec +72: =============================================================================== +72: All tests passed (91 assertions in 5 test cases) +72: + 66/208 Test #72: substructTestCatch ..................... Passed 0.65 sec test 74 Start 74: testReaction 74: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction 74: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 74: Test timeout computed to be: 1500 +73: =============================================================================== +73: All tests passed (490 assertions in 18 test cases) +73: + 67/208 Test #73: testGenericGroups ...................... Passed 0.10 sec +test 75 + Start 75: testReactionFingerprints + +75: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints +75: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +75: Test timeout computed to be: 1500 +75: [07:09:23] ------------------------------------- +75: [07:09:23] Test Reaction StructuralFingerprint 74: smi: O=C1CNC(=O)CN1 74: 1: O=C1CNC(=O)CN1 74: 2: COOC -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -74: [20:17:17] 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: [07:09:23] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +74: [07:09:23] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 74: O=C1CNC(=O)CN1 -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] mapped atoms in the reactants were not mapped in the products. +75: [07:09:23] ------------------------------------- +75: [07:09:23] Test Reaction DifferenceFingerprint +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 4 -74: [20:17:17] atom 0 in product 0 has multiple charge specifications. + 68/208 Test #75: testReactionFingerprints ............... Passed 0.15 sec +test 76 + Start 76: testEnumeration + +76: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration +76: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +76: Test timeout computed to be: 1500 +74: [07:09:24] atom 0 in product 0 has multiple charge specifications. 74: mass: 15.0001 74: Oc1ccccn1 74: Oc1ccc[nH]1 -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -74: [20:17:17] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: ([C:2] -74: [20:17:17] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -74: [20:17:17] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: [C:2]) -74: [20:17:17] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -74: [20:17:17] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -74: [20:17:17] 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: [20:17:17] reactant 2 has no mapped atoms. -74: [20:17:17] >> Atoms within one molecule have different RXN roles. -74: [20:17:17] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -74: [20:17:17] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: ([C:2] -74: [20:17:17] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -74: [20:17:17] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -74: [20:17:17] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -74: [20:17:17] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -74: [20:17:17] reactant 0 has no mapped atoms. -74: [20:17:17] reactant 1 has no mapped atoms. -74: [20:17:17] reactant 3 has no mapped atoms. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 5 found multiple times. -74: [20:17:17] product atom-mapping number 6 found multiple times. -74: [20:17:17] product atom-mapping number 7 found multiple times. -74: [20:17:17] product atom-mapping number 8 found multiple times. -74: [20:17:17] product atom-mapping number 12 found multiple times. -74: [20:17:17] product atom-mapping number 9 found multiple times. -74: [20:17:17] product atom-mapping number 10 found multiple times. -74: [20:17:17] product atom-mapping number 11 found multiple times. -74: [20:17:17] reactant 0 has no mapped atoms. -74: [20:17:17] reactant 1 has no mapped atoms. -74: [20:17:17] reactant 3 has no mapped atoms. -74: [20:17:17] reactant atom-mapping number 19 found multiple times. -74: [20:17:17] reactant atom-mapping number 25 found multiple times. -74: [20:17:17] reactant atom-mapping number 20 found multiple times. -74: [20:17:17] reactant atom-mapping number 21 found multiple times. -74: [20:17:17] reactant atom-mapping number 22 found multiple times. -74: [20:17:17] reactant atom-mapping number 23 found multiple times. -74: [20:17:17] reactant atom-mapping number 24 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. +74: [07:09:24] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +74: [07:09:24] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +74: [07:09:24] SMARTS Parse Error: syntax error while parsing: ([C:2] +74: [07:09:24] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +74: [07:09:24] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +74: [07:09:24] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +74: [07:09:24] SMARTS Parse Error: syntax error while parsing: [C:2]) +74: [07:09:24] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +74: [07:09:24] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +74: [07:09:24] 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: [07:09:24] reactant 2 has no mapped atoms. +74: [07:09:24] >> Atoms within one molecule have different RXN roles. +74: [07:09:24] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +74: [07:09:24] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +74: [07:09:24] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +74: [07:09:24] SMARTS Parse Error: syntax error while parsing: ([C:2] +74: [07:09:24] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +74: [07:09:24] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +74: [07:09:24] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +74: [07:09:24] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +74: [07:09:24] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +74: [07:09:24] reactant 0 has no mapped atoms. +74: [07:09:24] reactant 1 has no mapped atoms. +74: [07:09:24] reactant 3 has no mapped atoms. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 5 found multiple times. +74: [07:09:24] product atom-mapping number 6 found multiple times. +74: [07:09:24] product atom-mapping number 7 found multiple times. +74: [07:09:24] product atom-mapping number 8 found multiple times. +74: [07:09:24] product atom-mapping number 12 found multiple times. +74: [07:09:24] product atom-mapping number 9 found multiple times. +74: [07:09:24] product atom-mapping number 10 found multiple times. +74: [07:09:24] product atom-mapping number 11 found multiple times. +74: [07:09:24] reactant 0 has no mapped atoms. +74: [07:09:24] reactant 1 has no mapped atoms. +74: [07:09:24] reactant 3 has no mapped atoms. +74: [07:09:24] reactant atom-mapping number 19 found multiple times. +74: [07:09:24] reactant atom-mapping number 25 found multiple times. +74: [07:09:24] reactant atom-mapping number 20 found multiple times. +74: [07:09:24] reactant atom-mapping number 21 found multiple times. +74: [07:09:24] reactant atom-mapping number 22 found multiple times. +74: [07:09:24] reactant atom-mapping number 23 found multiple times. +74: [07:09:24] reactant atom-mapping number 24 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. 74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. 74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [20:17:17] product atom-mapping number 5 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 5 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 5 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 5 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. 74: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [20:17:17] product atom-mapping number 5 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 5 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 5 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 5 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. 74: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. 74: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. 74: F[C@](Cl)(Br)O[C@](F)(Cl)Br -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 4 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] mapped atoms in the reactants were not mapped in the products. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 4 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 4 -74: [20:17:17] product atom-mapping number 3 found multiple times. -74: [20:17:17] product atom-mapping number 2 found multiple times. -74: [20:17:17] product atom-mapping number 1 found multiple times. -74: [20:17:17] mapped atoms in the reactants were not mapped in the products. +74: [07:09:24] product atom-mapping number 3 found multiple times. +74: [07:09:24] product atom-mapping number 2 found multiple times. +74: [07:09:24] product atom-mapping number 1 found multiple times. +74: [07:09:24] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 4 -74: [20:17:17] product atom-mapping number 6 not found in reactants. -74: [20:17:17] product atom-mapping number 7 not found in reactants. -74: [20:17:17] product atom-mapping number 8 not found in reactants. -74: [20:17:17] product atom-mapping number 7 not found in reactants. -74: [20:17:17] product atom-mapping number 8 not found in reactants. -74: [20:17:17] product atom-mapping number 9 not found in reactants. -74: [20:17:17] product atom-mapping number 10 not found in reactants. -74: [20:17:17] mapped atoms in the reactants were not mapped in the products. +74: [07:09:24] product atom-mapping number 6 not found in reactants. +74: [07:09:24] product atom-mapping number 7 not found in reactants. +74: [07:09:24] product atom-mapping number 8 not found in reactants. +74: [07:09:24] product atom-mapping number 7 not found in reactants. +74: [07:09:24] product atom-mapping number 8 not found in reactants. +74: [07:09:24] product atom-mapping number 9 not found in reactants. +74: [07:09:24] product atom-mapping number 10 not found in reactants. +74: [07:09:24] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 6 -74: [20:17:17] product atom-mapping number 7 not found in reactants. -74: [20:17:17] product atom-mapping number 8 not found in reactants. -74: [20:17:17] product atom-mapping number 9 not found in reactants. -74: [20:17:17] product atom-mapping number 10 not found in reactants. -74: [20:17:17] mapped atoms in the reactants were not mapped in the products. +74: [07:09:24] product atom-mapping number 7 not found in reactants. +74: [07:09:24] product atom-mapping number 8 not found in reactants. +74: [07:09:24] product atom-mapping number 9 not found in reactants. +74: [07:09:24] product atom-mapping number 10 not found in reactants. +74: [07:09:24] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 6 74: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 74: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -74: [20:17:18] mapped atoms in the reactants were not mapped in the products. +74: [07:09:24] 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: [20:17:18] product atom-mapping number 17 not found in reactants. -74: [20:17:18] product atom-mapping number 18 not found in reactants. -74: [20:17:18] mapped atoms in the reactants were not mapped in the products. +74: [07:09:24] product atom-mapping number 17 not found in reactants. +74: [07:09:24] product atom-mapping number 18 not found in reactants. +74: [07:09:24] mapped atoms in the reactants were not mapped in the products. 74: unmapped numbers are: 12 -72: =============================================================================== -72: All tests passed (91 assertions in 5 test cases) -72: - 67/208 Test #72: substructTestCatch ..................... Passed 3.14 sec -test 75 - Start 75: testReactionFingerprints - -75: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints -75: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -75: Test timeout computed to be: 1500 -75: [20:17:19] ------------------------------------- -75: [20:17:19] Test Reaction StructuralFingerprint -75: [20:17:19] ------------------------------------- -75: [20:17:19] Test Reaction DifferenceFingerprint - 68/208 Test #75: testReactionFingerprints ............... Passed 0.10 sec -test 76 - Start 76: testEnumeration - -76: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration -76: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -76: Test timeout computed to be: 1500 -74: [20:17:19] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -74: [20:17:19] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +76: 30000000 30000000 +74: [07:09:24] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +74: [07:09:24] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 74: -74: [20:17:19] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +74: [07:09:24] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 74: ------------- 74: CCOc1ccccc1 -76: 30000000 30000000 -74: [20:17:22] reactant 0 has no mapped atoms. -74: [20:17:22] product 0 has no mapped atoms. -74: [20:17:22] 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 5.38 sec +74: [07:09:24] reactant 0 has no mapped atoms. +74: [07:09:24] product 0 has no mapped atoms. +74: [07:09:24] 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 1.14 sec test 77 Start 77: rxnTestCatch 77: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 77: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 77: Test timeout computed to be: 1500 -77: [20:17:23] atom 0 in product 0 has multiple charge specifications. -77: [20:17:23] mapped atoms in the reactants were not mapped in the products. +77: [07:09:25] atom 0 in product 0 has multiple charge specifications. +77: [07:09:25] mapped atoms in the reactants were not mapped in the products. 77: unmapped numbers are: 2 -77: [20:17:23] mapped atoms in the reactants were not mapped in the products. +77: [07:09:25] mapped atoms in the reactants were not mapped in the products. 77: unmapped numbers are: 2 -77: [20:17:23] SMARTS Parse Error: unclosed ring for input: 'CC1' -77: [20:17:23] SMILES Parse Error: unclosed ring for input: 'CC1' -77: [20:17:23] mapped atoms in the reactants were not mapped in the products. +77: [07:09:25] SMARTS Parse Error: unclosed ring for input: 'CC1' +77: [07:09:25] SMILES Parse Error: unclosed ring for input: 'CC1' +77: [07:09:25] mapped atoms in the reactants were not mapped in the products. 77: unmapped numbers are: 2 -77: [20:17:23] product atom-mapping number 2 not found in reactants. -77: [20:17:23] mapped atoms in the reactants were not mapped in the products. +77: [07:09:25] product atom-mapping number 2 not found in reactants. +77: [07:09:25] mapped atoms in the reactants were not mapped in the products. 77: unmapped numbers are: 2 -77: [20:17:23] product atom-mapping number 2 not found in reactants. -77: [20:17:23] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +77: [07:09:25] product atom-mapping number 2 not found in reactants. +77: [07:09:25] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 77: =============================================================================== 77: All tests passed (450 assertions in 14 test cases) 77: - 70/208 Test #77: rxnTestCatch ........................... Passed 0.99 sec + 70/208 Test #77: rxnTestCatch ........................... Passed 0.17 sec test 78 Start 78: pyChemReactions 78: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 78: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 78: Test timeout computed to be: 1500 -25: Checking against /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -25: All 191 tests passed - 71/208 Test #39: resMolSupplierTest ..................... Passed 32.12 sec + 71/208 Test #39: resMolSupplierTest ..................... Passed 7.50 sec test 79 Start 79: pyChemReactionEnumerations 79: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 79: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 79: Test timeout computed to be: 1500 -25: -25: Computing MMFF94 energies for /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -78: [20:17:27] +78: [07:09:25] 78: 78: **** 78: Pre-condition Violation @@ -21199,7 +21236,7 @@ 78: Failed Expression: d_implicitValence > -1 78: **** 78: -78: [20:17:27] +78: [07:09:25] 78: 78: **** 78: Pre-condition Violation @@ -21208,88 +21245,83 @@ 78: Failed Expression: d_implicitValence > -1 78: **** 78: -78: ...[20:17:27] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [20:17:27] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [20:17:27] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: [20:17:27] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -78: .[20:17:27] product atom-mapping number 1 found multiple times. -78: [20:17:27] product atom-mapping number 1 found multiple times. -78: ................[20:17:27] mapped atoms in the reactants were not mapped in the products. +78: ...[07:09:25] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [07:09:25] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [07:09:25] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: [07:09:25] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +78: .[07:09:25] product atom-mapping number 1 found multiple times. +25: Checking against /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +78: [07:09:25] product atom-mapping number 1 found multiple times. +78: ................[07:09:25] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -78: [20:17:27] mapped atoms in the reactants were not mapped in the products. +78: [07:09:25] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 -78: .[20:17:27] mapped atoms in the reactants were not mapped in the products. +78: .[07:09:25] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 3 78: ../build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:515: DeprecationWarning: Please use assertTrue instead. 78: self.failUnless(rxn) -78: [20:17:27] reactant 2 has no mapped atoms. -78: [20:17:27] reactant 2 has no mapped atoms. -78: [20:17:27] product 1 has no mapped atoms. +78: [07:09:25] reactant 2 has no mapped atoms. +78: [07:09:25] reactant 2 has no mapped atoms. +78: [07:09:25] product 1 has no mapped atoms. 78: ../build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:558: DeprecationWarning: Please use assertEqual instead. 78: self.assertEquals(res, res2) -78: ......[20:17:27] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -78: [20:17:27] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -78: [20:17:27] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -78: [20:17:27] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -78: .[20:17:27] reactant atom-mapping number 1 found multiple times. -78: [20:17:27] product atom-mapping number 2 not found in reactants. -78: [20:17:27] mapped atoms in the reactants were not mapped in the products. +78: ......[07:09:25] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +78: [07:09:25] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +78: [07:09:25] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +78: [07:09:25] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +78: .[07:09:25] reactant atom-mapping number 1 found multiple times. +78: [07:09:25] product atom-mapping number 2 not found in reactants. +78: [07:09:25] mapped atoms in the reactants were not mapped in the products. 78: unmapped numbers are: 4 -78: [20:17:27] product atom-mapping number 5 not found in reactants. +78: [07:09:25] product atom-mapping number 5 not found in reactants. +58: [07:09:26] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:26] Warning: molecule is tagged as 3D, but all Z coords are zero 78: ........./build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:739: DeprecationWarning: Please use assertFalse instead. 78: self.failIf(rxn is None) 78: /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> 78: png = open(fname, 'rb').read() 78: ResourceWarning: Enable tracemalloc to get the object allocation traceback -78: ..[20:17:27] SMARTS Parse Error: syntax error while parsing: boromicacid -78: [20:17:27] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -78: [20:17:27] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -78: [20:17:27] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -78: [20:17:27] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -78: [20:17:27] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -78: [20:17:27] reaction has no reactants -78: [20:17:27] reaction has no products -78: [20:17:27] initialization failed -78: [20:17:27] reaction has no reactants -78: [20:17:27] reaction has no products -78: .[20:17:27] SMARTS Parse Error: syntax error while parsing: boromicacid -78: [20:17:27] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -78: [20:17:27] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -78: [20:17:27] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -78: [20:17:27] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -78: [20:17:27] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -78: [20:17:27] reaction has no reactants -78: [20:17:27] reaction has no products -78: [20:17:27] initialization failed -78: [20:17:27] reaction has no reactants -78: [20:17:27] reaction has no products +25: All 191 tests passed +78: ..[07:09:26] SMARTS Parse Error: syntax error while parsing: boromicacid +78: [07:09:26] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +78: [07:09:26] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +78: [07:09:26] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +78: [07:09:26] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +78: [07:09:26] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +78: [07:09:26] reaction has no reactants +78: [07:09:26] reaction has no products +78: [07:09:26] initialization failed +78: [07:09:26] reaction has no reactants +78: [07:09:26] reaction has no products +78: .[07:09:26] SMARTS Parse Error: syntax error while parsing: boromicacid +78: [07:09:26] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +78: [07:09:26] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +78: [07:09:26] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +78: [07:09:26] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +78: [07:09:26] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +78: [07:09:26] reaction has no reactants +78: [07:09:26] reaction has no products +78: [07:09:26] initialization failed +78: [07:09:26] reaction has no reactants +78: [07:09:26] reaction has no products 78: . 78: ---------------------------------------------------------------------- -78: Ran 45 tests in 0.617s +78: Ran 45 tests in 0.308s 78: 78: OK 78: ******************************************** 78: /build/rdkit-202209.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -78: -58: [20:17:28] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:28] Warning: molecule is tagged as 3D, but all Z coords are zero - 72/208 Test #78: pyChemReactions ........................ Passed 5.09 sec -test 80 - Start 80: pyChemReactionSanitize - -80: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" -80: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap -80: Test timeout computed to be: 1500 -79: [20:17:29] == testCartesianProduct +78: +79: [07:09:26] == testCartesianProduct 79: /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:62: DeprecationWarning: Please use assertEqual instead. 79: self.assertEquals(cartProd.GetNumPermutations(), 10*5*6) -79: .[20:17:29] == testEnumerateLibrary +79: .[07:09:26] == testEnumerateLibrary 79: /build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:268: ResourceWarning: unclosed file <_io.BufferedReader name='/build/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 58: ---------------------------------- 58: ---------------------------------- -58: [20:17:29] +58: [07:09:26] 58: 58: **** 58: Pre-condition Violation @@ -21298,74 +21330,83 @@ 58: Failed Expression: rlabel >= 0 && rlabel < 100 58: **** 58: -58: [20:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -79: ..[20:17:29] == testRGroupState -79: .[20:17:29] == testRandomEnumerateAllBBsLibrary +58: [07:09:26] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +79: ..[07:09:26] == testRGroupState + 72/208 Test #78: pyChemReactions ........................ Passed 1.16 sec +test 80 + Start 80: pyChemReactionSanitize + +80: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" +80: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap +80: Test timeout computed to be: 1500 +79: .[07:09:26] == testRandomEnumerateAllBBsLibrary 79: ** [1, 1] 79: ** [0, 2] 79: ** [1, 0] -79: .[20:17:30] == testRandomEnumerateLibrary -79: .[20:17:30] == testRandomSample -79: .[20:17:30] == testRandomSampleAllBBs -79: .[20:17:30] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -79: [20:17:30] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -79: .[20:17:30] == testRemoveBadMatches -79: .[20:17:30] == testTimings -80: .[20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. +25: +25: Computing MMFF94 energies for /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +79: .[07:09:26] == testRandomEnumerateLibrary +79: .[07:09:26] == testRandomSample +79: .[07:09:26] == testRandomSampleAllBBs +79: .[07:09:26] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +79: [07:09:26] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +79: .[07:09:26] == testRemoveBadMatches +79: .[07:09:26] == testTimings +80: .[07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. 80: ./build/rdkit-202209.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py:287: DeprecationWarning: Please use assertEqual instead. 80: self.assertEquals(res, good_res) -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] reactant 0 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] product 0 has no mapped atoms. -80: [20:17:32] Could not find RLabel mapping for atom: 0 in template: 1 -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. -80: [20:17:32] reactant 1 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] reactant 0 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] product 0 has no mapped atoms. +80: [07:09:26] Could not find RLabel mapping for atom: 0 in template: 1 +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. +80: [07:09:26] reactant 1 has no mapped atoms. 80: () 80: ******************************************** 80: $RXN @@ -21685,7 +21726,7 @@ 80: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 80: .. 80: ---------------------------------------------------------------------- -80: Ran 4 tests in 0.186s +80: Ran 4 tests in 0.046s 80: 80: OK 80: $RXN @@ -21732,15 +21773,19 @@ 80: M END 80: 80: $RXN Failed -58: [20:17:32] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -58: [20:17:32] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' - 73/208 Test #80: pyChemReactionSanitize ................. Passed 4.10 sec +58: [07:09:26] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +58: [07:09:26] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' + 73/208 Test #80: pyChemReactionSanitize ................. Passed 0.75 sec test 81 Start 81: testChemTransforms 81: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 81: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 81: Test timeout computed to be: 1500 +58: [07:09:27] Empty atom list: 'M ALS 1 0 F' on line 8. +58: de_DE.UTF-8 +58: [07:09:27] ------------------------------------- +58: [07:09:27] Test multithreading Locale Switching 81: 1 smi: CC 81: 1 smi: CC 81: 2 smi: CCO[C@H](N)P @@ -21749,38 +21794,19 @@ 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 -58: [20:17:33] Empty atom list: 'M ALS 1 0 F' on line 8. -81: [20:17:33] SMARTS Parse Error: syntax error while parsing: bar -81: [20:17:33] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -58: de_DE.UTF-8 -58: [20:17:33] ------------------------------------- -58: [20:17:33] Test multithreading Locale Switching -58: [20:17:33] Test multithreading (Done) -58: [20:17:33] ------------------------------------- -58: *************************************** -58: *************************************** -58: [20:17:33] bond with order 0 found on line 7. This is not part of the MDL specification. -58: [20:17:33] unrecognized query bond type, 9, found on line 7. Using an "any" query. - 74/208 Test #81: testChemTransforms ..................... Passed 0.77 sec +81: [07:09:27] SMARTS Parse Error: syntax error while parsing: bar +81: [07:09:27] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' + 74/208 Test #81: testChemTransforms ..................... Passed 0.16 sec test 82 Start 82: chemTransformsTestCatch 82: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 82: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 82: Test timeout computed to be: 1500 -58: [20:17:33] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -58: [20:17:33] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -58: [20:17:33] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:33] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:33] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:33] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:33] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:33] Warning: molecule is tagged as 3D, but all Z coords are zero -58: generating smiles -58: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -58: converting back -82: [20:17:34] Incomplete atom labelling, cannot make bond -82: [20:17:34] +58: [07:09:27] Test multithreading (Done) +58: [07:09:27] ------------------------------------- +82: [07:09:27] Incomplete atom labelling, cannot make bond +82: [07:09:27] 82: 82: **** 82: Invariant Violation @@ -21789,9 +21815,10 @@ 82: Failed Expression: !bond.b 82: **** 82: -58: check isomorphism -82: [20:17:34] Incomplete atom labelling, cannot make bond -82: [20:17:34] +58: *************************************** +58: *************************************** +82: [07:09:27] Incomplete atom labelling, cannot make bond +82: [07:09:27] 82: 82: **** 82: Invariant Violation @@ -21800,8 +21827,8 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [20:17:34] Incomplete atom labelling, cannot make bond -82: [20:17:34] +82: [07:09:27] Incomplete atom labelling, cannot make bond +82: [07:09:27] 82: 82: **** 82: Invariant Violation @@ -21810,10 +21837,12 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [20:17:34] Incomplete atom labelling, cannot make bond -82: [20:17:34] Incomplete atom labelling, cannot make bond -82: [20:17:34] Incomplete atom labelling, cannot make bond -82: [20:17:34] +58: [07:09:27] bond with order 0 found on line 7. This is not part of the MDL specification. +58: [07:09:27] unrecognized query bond type, 9, found on line 7. Using an "any" query. +82: [07:09:27] Incomplete atom labelling, cannot make bond +82: [07:09:27] Incomplete atom labelling, cannot make bond +82: [07:09:27] Incomplete atom labelling, cannot make bond +82: [07:09:27] 82: 82: **** 82: Invariant Violation @@ -21822,8 +21851,16 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [20:17:34] Incomplete atom labelling, cannot make bond -82: [20:17:34] +58: [07:09:27] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +58: [07:09:27] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +58: [07:09:27] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:27] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:27] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:27] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:27] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:27] Warning: molecule is tagged as 3D, but all Z coords are zero +82: [07:09:27] Incomplete atom labelling, cannot make bond +82: [07:09:27] 82: 82: **** 82: Invariant Violation @@ -21832,7 +21869,7 @@ 82: Failed Expression: !bond.b 82: **** 82: -82: [20:17:34] +82: [07:09:27] 82: 82: **** 82: Invariant Violation @@ -21844,26 +21881,21 @@ 82: =============================================================================== 82: All tests passed (531 assertions in 4 test cases) 82: - 75/208 Test #82: chemTransformsTestCatch ................ Passed 1.07 sec + 75/208 Test #82: chemTransformsTestCatch ................ Passed 0.20 sec test 83 Start 83: tautomerQueryTestCatch 83: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 83: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery 83: Test timeout computed to be: 1500 -61: [20:17:35] Finished: testSmiCorrectness() -61: [20:17:35] ----------------------------------------- -61: -61: [20:17:35] -61: ----------------------------------------- -61: [20:17:35] Spurious data before the first property will be ignored -61: [20:17:35] Property will be truncated after the first blank line -61: [20:17:35] Property will be truncated after the first blank line -61: [20:17:35] Property will be truncated after the first blank line +58: generating smiles +58: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +58: converting back +58: check isomorphism 83: =============================================================================== 83: All tests passed (86 assertions in 12 test cases) 83: - 76/208 Test #83: tautomerQueryTestCatch ................. Passed 1.44 sec + 76/208 Test #83: tautomerQueryTestCatch ................. Passed 0.41 sec test 84 Start 84: pyTautomerQuery @@ -21872,7 +21904,7 @@ 84: Test timeout computed to be: 1500 79: . 79: ---------------------------------------------------------------------- -79: Ran 11 tests in 8.477s +79: Ran 11 tests in 1.930s 79: 79: OK 79: True @@ -21885,13 +21917,10 @@ 79: 0 10 out of 10 79: 1 5 out of 5 79: 2 6 out of 6 -79: Skipped 10000000 in 0.5506429672241211 seconds -79: Skipped 10000000 in 4.082797527313232 seconds -79: Skipped 10000000 in 0.9184465408325195 seconds -61: [20:17:37] Finished: testSDCorrectness() -61: [20:17:37] ----------------------------------------- -61: - 77/208 Test #61: testMultithreadedMolSupplier ........... Passed 31.74 sec +79: Skipped 10000000 in 0.1051492691040039 seconds +79: Skipped 10000000 in 0.9495666027069092 seconds +79: Skipped 10000000 in 0.26621174812316895 seconds + 77/208 Test #79: pyChemReactionEnumerations ............. Passed 2.67 sec test 85 Start 85: testSubgraphs1 @@ -21906,7 +21935,24 @@ 85: Finished 85: ----------------------- 85: testSubgraphs2 - 78/208 Test #79: pyChemReactionEnumerations ............. Passed 12.28 sec +85: Finished +85: ----------------------- +85: Path retrieval +85: Finished +85: ----------------------- +85: Path retrieval2 +85: Finished +85: ----------------------- +85: Unique Subgraph retrieval +85: Finished +85: ----------------------- +85: testUniqueSubgraphs2 +84: ..... +84: ---------------------------------------------------------------------- +84: Ran 5 tests in 0.091s +84: +84: OK + 78/208 Test #84: pyTautomerQuery ........................ Passed 0.75 sec test 86 Start 86: testSubgraphs2 @@ -21928,25 +21974,13 @@ 86: ----------------------- 86: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 86: Finished - 79/208 Test #86: testSubgraphs2 ......................... Passed 0.21 sec + 79/208 Test #86: testSubgraphs2 ......................... Passed 0.04 sec test 87 Start 87: filterCatalogTest 87: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 87: Working Directory: /build/rdkit-202209.3/obj-aarch64-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 87: Warning: molecule failed filter 87: Warning: molecule failed filter: reason hzone_phenol_A(479) 87: v = { @@ -22035,53 +22069,41 @@ 87: 10,15}, 87: 11,16}, 87: } -84: ..... -84: ---------------------------------------------------------------------- -84: Ran 5 tests in 0.516s -84: -84: OK -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 -87: 0 hzone_phenol_A(479) -87: 1 cyano_imine_B(17) -87: 2 keto_keto_gamma(5) - 80/208 Test #87: filterCatalogTest ...................... Passed 0.83 sec +85: Finished +85: ----------------------- +85: testRootedSubgraphs +85: Finished +85: ----------------------- +85: testRootedPaths +85: Finished + 80/208 Test #85: testSubgraphs1 ......................... Passed 0.58 sec test 88 Start 88: pyFilterCatalog 88: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 88: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 88: Test timeout computed to be: 1500 - 81/208 Test #84: pyTautomerQuery ........................ Passed 3.55 sec +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 +87: 0 hzone_phenol_A(479) +87: 1 cyano_imine_B(17) +87: 2 keto_keto_gamma(5) + 81/208 Test #87: filterCatalogTest ...................... Passed 0.39 sec test 89 Start 89: testFragCatalog 89: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog 89: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog 89: Test timeout computed to be: 1500 -85: Finished -85: ----------------------- -85: testRootedSubgraphs -85: Finished -85: ----------------------- -85: testRootedPaths -85: Finished - 82/208 Test #85: testSubgraphs1 ......................... Passed 1.77 sec -test 90 - Start 90: pyFragCatalog - -90: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" -90: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap -90: Test timeout computed to be: 1500 89: 21 -58: [20:17:41] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [20:17:41] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [20:17:41] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [20:17:41] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. -58: [20:17:41] deprecated group abbreviation ignored on line 24 +58: [07:09:29] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [07:09:29] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [07:09:29] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [07:09:29] Warning: conflicting stereochemistry at atom 1 ignored. by rule 1a. +58: [07:09:29] 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: [20:17:41] +58: [07:09:29] 58: 58: **** 58: Post-condition Violation @@ -22092,157 +22114,135 @@ 58: 88: ../build/rdkit-202209.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py:172: DeprecationWarning: Please use assertEqual instead. 88: self.assertEquals(entry.GetProp(key), "PAINS_A") -90: ......... -90: ---------------------------------------------------------------------- -90: Ran 9 tests in 0.346s -90: -90: OK - 83/208 Test #90: pyFragCatalog .......................... Passed 3.12 sec -test 91 - Start 91: testDescriptors +89: [07:09:30] +89: +89: **** +89: Invariant Violation +89: nonsense +89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +89: Failed Expression: token != tokens.end() +89: **** +89: +89: [07:09:30] +89: +89: **** +89: Invariant Violation +89: nonsense no new line +89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +89: Failed Expression: token != tokens.end() +89: **** +89: +89: [07:09:30] +89: +89: **** +89: Invariant Violation +89: nonsense with tab +89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +89: Failed Expression: token != tokens.end() +89: **** +89: + 82/208 Test #89: testFragCatalog ........................ Passed 1.87 sec +test 90 + Start 90: pyFragCatalog -91: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -91: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -91: Test timeout computed to be: 1500 -91: [20:17:42] ------------------------------------- -91: [20:17:42] Test Crippen parameter acquisition. -91: [20:17:42] done -91: [20:17:42] ------------------------------------- -91: [20:17:42] Test Crippen calculation. -91: [20:17:42] done -91: [20:17:42] ------------------------------------- -91: [20:17:42] Test Issue262: problems with Crippen calculation from pickles. -91: [20:17:42] done -91: [20:17:42] ------------------------------------- -91: [20:17:42] Test AMW calculation. -91: [20:17:42] done -91: [20:17:42] ------------------------------------- -91: [20:17:42] Test Exact MW calculation. -91: [20:17:42] done -91: [20:17:42] ------------------------------------- -91: [20:17:42] Test Labute ASA descriptors. -91: [20:17:42] done -91: [20:17:42] ------------------------------------- -91: [20:17:42] Test TPSA descriptors. -91: [20:17:43] done -91: [20:17:43] ------------------------------------- -91: [20:17:43] Test Lipinski parameters. -91: [20:17:44] done -91: [20:17:44] ------------------------------------- -91: [20:17:44] Test VSA descriptors. -91: [20:17:44] done -91: [20:17:44] ------------------------------------- -91: [20:17:44] Test molecular formula calculation. -91: [20:17:44] done -91: [20:17:44] ------------------------------------- -91: [20:17:44] Test Issue 3415534. -91: [20:17:44] done -91: [20:17:44] ------------------------------------- -91: [20:17:44] Test Issue3433771: Bad definition for Crippen atom type O11. -91: [20:17:44] done -91: [20:17:44] ------------------------------------- -91: [20:17:44] Test multithreading -91: reading molecules -91: processing -91: launch :0 -91: launch :1 -91: launch :2 -91: launch :3 -88: ...........[20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: [20:17:48] SMILES Parse Error: syntax error while parsing: --- -88: [20:17:48] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -88: [20:17:48] dasfsadf -88: .[20:17:49] SMILES Parse Error: syntax error while parsing: mydoghasfleas -88: [20:17:49] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +90: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" +90: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap +90: Test timeout computed to be: 1500 +88: ...........[07:09:30] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:30] dasfsadf +88: [07:09:30] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:30] dasfsadf +88: [07:09:30] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:30] dasfsadf +88: [07:09:30] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:30] dasfsadf +88: [07:09:30] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:30] dasfsadf +88: [07:09:30] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:30] dasfsadf +88: [07:09:30] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:30] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:30] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: [07:09:31] SMILES Parse Error: syntax error while parsing: --- +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +88: [07:09:31] dasfsadf +88: .[07:09:31] SMILES Parse Error: syntax error while parsing: mydoghasfleas +88: [07:09:31] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' 88: ...... 88: ---------------------------------------------------------------------- -88: Ran 20 tests in 7.765s +88: Ran 20 tests in 1.849s 88: 88: OK 88: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -22264,271 +22264,249 @@ 88: 1 88: 2 88: running - 84/208 Test #88: pyFilterCatalog ........................ Passed 10.82 sec + 83/208 Test #88: pyFilterCatalog ........................ Passed 2.65 sec +test 91 + Start 91: testDescriptors + +91: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +91: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +91: Test timeout computed to be: 1500 +91: [07:09:31] ------------------------------------- +91: [07:09:31] Test Crippen parameter acquisition. +91: [07:09:31] done +91: [07:09:31] ------------------------------------- +91: [07:09:31] Test Crippen calculation. +91: [07:09:31] done +91: [07:09:31] ------------------------------------- +91: [07:09:31] Test Issue262: problems with Crippen calculation from pickles. +91: [07:09:31] done +91: [07:09:31] ------------------------------------- +91: [07:09:31] Test AMW calculation. +91: [07:09:31] done +91: [07:09:31] ------------------------------------- +91: [07:09:31] Test Exact MW calculation. +91: [07:09:31] done +91: [07:09:31] ------------------------------------- +91: [07:09:31] Test Labute ASA descriptors. +91: [07:09:31] done +91: [07:09:31] ------------------------------------- +91: [07:09:31] Test TPSA descriptors. +90: ......... +90: ---------------------------------------------------------------------- +90: Ran 9 tests in 0.137s +90: +90: OK +91: [07:09:31] done +91: [07:09:31] ------------------------------------- +91: [07:09:31] Test Lipinski parameters. + 84/208 Test #90: pyFragCatalog .......................... Passed 0.84 sec test 92 Start 92: testAUTOCORR2D 92: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 92: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 92: Test timeout computed to be: 1500 -89: [20:17:50] -89: -89: **** -89: Invariant Violation -89: nonsense -89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -89: Failed Expression: token != tokens.end() -89: **** -89: -89: [20:17:50] -89: -89: **** -89: Invariant Violation -89: nonsense no new line -89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -89: Failed Expression: token != tokens.end() -89: **** -89: -92: [20:17:50] ---------------------------- +92: [07:09:31] ---------------------------- 92: start test autocorr2D -89: [20:17:50] -89: -89: **** -89: Invariant Violation -89: nonsense with tab -89: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -89: Failed Expression: token != tokens.end() -89: **** -89: - 85/208 Test #89: testFragCatalog ........................ Passed 10.48 sec +91: [07:09:32] done +91: [07:09:32] ------------------------------------- +91: [07:09:32] Test VSA descriptors. +91: [07:09:32] done +91: [07:09:32] ------------------------------------- +91: [07:09:32] Test molecular formula calculation. +91: [07:09:32] done +91: [07:09:32] ------------------------------------- +91: [07:09:32] Test Issue 3415534. +91: [07:09:32] done +91: [07:09:32] ------------------------------------- +91: [07:09:32] Test Issue3433771: Bad definition for Crippen atom type O11. +91: [07:09:32] done +91: [07:09:32] ------------------------------------- +91: [07:09:32] Test multithreading +91: reading molecules +91: processing +91: launch :0 +91: launch :1 +91: launch :2 +91: launch :3 +92: [07:09:32] done +92: [07:09:32] ------------------------------------- +92: [07:09:32] Test Github #3806: NaNs from AUTOCORR2D descriptor +92: [07:09:32] done + 85/208 Test #92: testAUTOCORR2D ......................... Passed 0.69 sec test 93 Start 93: testATF 93: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF 93: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 93: Test timeout computed to be: 1500 - 86/208 Test #93: testATF ................................ Passed 0.12 sec + 86/208 Test #93: testATF ................................ Passed 0.04 sec test 94 Start 94: testBCUT 94: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 94: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 94: Test timeout computed to be: 1500 -94: [20:17:50] ------------------------------------- -94: [20:17:50] Basic BCUT tests. -94: [20:17:50] done -94: [20:17:50] ------------------------------------- -94: [20:17:50] Larger BCUT tests. -92: [20:17:52] done -92: [20:17:52] ------------------------------------- -92: [20:17:52] Test Github #3806: NaNs from AUTOCORR2D descriptor -92: [20:17:52] done - 87/208 Test #92: testAUTOCORR2D ......................... Passed 2.82 sec +94: [07:09:32] ------------------------------------- +94: [07:09:32] Basic BCUT tests. +94: [07:09:32] done +94: [07:09:32] ------------------------------------- +94: [07:09:32] Larger BCUT tests. +61: [07:09:33] Finished: testSmiCorrectness() +61: [07:09:33] ----------------------------------------- +61: +61: [07:09:33] +61: ----------------------------------------- +58: [07:09:33] Warning: molecule is tagged as 3D, but all Z coords are zero +58: [07:09:33] Warning: molecule is tagged as 3D, but all Z coords are zero +61: [07:09:33] Spurious data before the first property will be ignored +61: [07:09:33] Property will be truncated after the first blank line +61: [07:09:33] Property will be truncated after the first blank line +61: [07:09:33] Property will be truncated after the first blank line +58: ---------------------------------- +58: ---------------------------------- +58: [07:09:33] +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: [07:09:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +58: [07:09:34] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +58: [07:09:34] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +58: [07:09:34] Empty atom list: 'M ALS 1 0 F' on line 8. + 87/208 Test #58: fileParsersTest1 ....................... Passed 13.84 sec test 95 Start 95: testEEM 95: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM 95: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 95: Test timeout computed to be: 1500 - 88/208 Test #94: testBCUT ............................... Passed 3.95 sec +61: [07:09:34] Finished: testSDCorrectness() +61: [07:09:34] ----------------------------------------- +61: + 88/208 Test #61: testMultithreadedMolSupplier ........... Passed 13.32 sec test 96 Start 96: testPBF 96: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF 96: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 96: Test timeout computed to be: 1500 -96: [20:17:54] ------------------------------------- -96: [20:17:54] Basic PBF tests. -96: [20:17:55] done -96: [20:17:55] ------------------------------------- -96: [20:17:55] PBF edge cases. -96: [20:17:55] done - 89/208 Test #96: testPBF ................................ Passed 1.27 sec +96: [07:09:34] ------------------------------------- +96: [07:09:34] Basic PBF tests. + 89/208 Test #94: testBCUT ............................... Passed 2.10 sec test 97 Start 97: testRDFcustom 97: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 97: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 97: Test timeout computed to be: 1500 +96: [07:09:34] done +96: [07:09:34] ------------------------------------- +96: [07:09:34] PBF edge cases. +96: [07:09:34] done + 90/208 Test #96: testPBF ................................ Passed 0.53 sec +test 98 + Start 98: testRDF + +98: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF +98: Working Directory: /build/rdkit-202209.3/obj-aarch64-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: 3.75174 s +95: Elapsed time: 1.23291 s 95: Errors:0 -95: [20:17:56] test on : 500 molecules done - 90/208 Test #95: testEEM ................................ Passed 4.00 sec -test 98 - Start 98: testRDF - -98: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF -98: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -98: Test timeout computed to be: 1500 -58: [20:17:57] Warning: molecule is tagged as 3D, but all Z coords are zero -58: [20:17:57] Warning: molecule is tagged as 3D, but all Z coords are zero -58: ---------------------------------- -58: ---------------------------------- -58: [20:17:57] -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: [20:17:57] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -97: =>start test rdf custom -97: [20:17:59] test on : 365 molecules done -98: =>start test rdf -98: [20:18:00] test on : 365 molecules done - 91/208 Test #98: testRDF ................................ Passed 3.70 sec +95: [07:09:35] test on : 500 molecules done + 91/208 Test #95: testEEM ................................ Passed 1.27 sec test 99 Start 99: testMORSE 99: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 99: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 99: Test timeout computed to be: 1500 -58: [20:18:00] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -58: [20:18:00] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -58: [20:18:01] Empty atom list: 'M ALS 1 0 F' on line 8. - 92/208 Test #58: fileParsersTest1 ....................... Passed 58.16 sec +97: =>start test rdf custom +97: [07:09:35] test on : 365 molecules done +98: =>start test rdf +98: [07:09:36] test on : 365 molecules done + 92/208 Test #98: testRDF ................................ Passed 1.38 sec test 100 Start 100: test3D 100: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 100: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 100: Test timeout computed to be: 1500 -100: [20:18:01] ------------------------------------- -100: [20:18:01] Basic PMI tests. -100: [20:18:03] done -100: [20:18:03] ------------------------------------- -100: [20:18:03] More PMI/NPR tests. -100: [20:18:03] done -100: [20:18:03] ------------------------------------- -100: [20:18:03] Basic NPR tests. -100: [20:18:05] done -100: [20:18:05] ------------------------------------- -100: [20:18:05] PMI edge cases. -100: [20:18:05] done -100: [20:18:05] ------------------------------------- -100: [20:18:05] NPR edge cases. -100: [20:18:05] done -100: [20:18:05] ------------------------------------- -100: [20:18:05] 3D descriptors. -100: [20:18:05] done -100: [20:18:05] ------------------------------------- -100: [20:18:05] 3D descriptor edge cases. -100: [20:18:05] done -100: [20:18:05] ------------------------------------- -100: [20:18:05] Inertial shape factor. -100: [20:18:05] done - 93/208 Test #100: test3D ................................. Passed 4.59 sec +100: [07:09:36] ------------------------------------- +100: [07:09:36] Basic PMI tests. +25: Checking against /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: +25: Computing MMFF94 energies for /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... +97: =>start test morse custom +97: [07:09:36] test on : 365 molecules done +100: [07:09:37] done +100: [07:09:37] ------------------------------------- +100: [07:09:37] More PMI/NPR tests. +100: [07:09:37] done +100: [07:09:37] ------------------------------------- +100: [07:09:37] Basic NPR tests. +99: =>start test MORSE +99: =>read file +99: [07:09:37] test on : 365 molecules done + 93/208 Test #99: testMORSE .............................. Passed 1.74 sec test 101 Start 101: testWHIM 101: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 101: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 -99: =>start test MORSE -99: =>read file -99: [20:18:06] test on : 365 molecules done - 94/208 Test #99: testMORSE .............................. Passed 5.89 sec +100: [07:09:37] done +100: [07:09:37] ------------------------------------- +100: [07:09:37] PMI edge cases. +100: [07:09:37] done +100: [07:09:37] ------------------------------------- +100: [07:09:37] NPR edge cases. +100: [07:09:37] done +100: [07:09:37] ------------------------------------- +100: [07:09:37] 3D descriptors. +100: [07:09:37] done +100: [07:09:37] ------------------------------------- +100: [07:09:37] 3D descriptor edge cases. +100: [07:09:37] done +100: [07:09:37] ------------------------------------- +100: [07:09:37] Inertial shape factor. +100: [07:09:37] done + 94/208 Test #100: test3D ................................. Passed 1.23 sec test 102 Start 102: testGETAWAY 102: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 102: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 -97: =>start test morse custom -97: [20:18:06] test on : 365 molecules done -25: Checking against /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +97: =>start test AUTOCORR3D custom +97: [07:09:37] test on : 365 molecules done 101: =>start test WHIM -101: [20:18:08] test on : 365 molecules done - 95/208 Test #101: testWHIM ............................... Passed 3.13 sec +101: [07:09:37] test on : 365 molecules done + 95/208 Test #101: testWHIM ............................... Passed 0.79 sec test 103 Start 103: testAUTOCORR3D 103: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 103: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 -25: All 191 tests passed -97: =>start test AUTOCORR3D custom -97: [20:18:10] test on : 365 molecules done -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test Issue252: Bad definitions for Crippen atom types. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test calculation of ChiVs. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test calculation of ChiNs. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test calculation of HallKierAlpha. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test calculation of Kappa1. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test calculation of Kappa2. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test calculation of Kappa3. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test Crippen atom type calculations. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test ring descriptors -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test other count descriptors. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test MQN -25: -25: Computing MMFF94 energies for /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test GitHub Issue 56. -91: [20:18:10] WARNING: not removing hydrogen atom without neighbors -91: [20:18:10] WARNING: not removing hydrogen atom without neighbors -91: [20:18:10] WARNING: not removing hydrogen atom without neighbors -91: [20:18:10] WARNING: not removing hydrogen atom without neighbors -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test Github92: Bad Crippen atom type for pyrrole H. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test Github362: order dependence in Kier-Hall descriptors. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test calculation of spiro and bridgehead counts. -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test Github694: ExactMolWt ignoring the mass of the electron -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Testing Properties and KitchenSink -91: [20:18:10] ---Caught keyerror (bad property name)--- -91: [20:18:10] ---Caught stereo value error--- -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test USR Descriptor -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test Github #1973: support P and S terms for TPSA calculation -91: [20:18:10] done -91: [20:18:10] ------------------------------------- -91: [20:18:10] Test Github #2948: Empty molecule has non-zero LabuteASA -91: [20:18:10] done - 96/208 Test #91: testDescriptors ........................ Passed 27.94 sec +97: =>start test 2 WHIM custom +97: [07:09:38] test on : 365 molecules done +97: =>start test 1 WHIM custom +97: [07:09:38] test on : 365 molecules done +103: =>start test autocorr3D +103: [07:09:39] test on : 365 molecules done + 96/208 Test #103: testAUTOCORR3D ......................... Passed 1.45 sec test 104 Start 104: testCoulombMat @@ -22537,7 +22515,7 @@ 104: Test timeout computed to be: 1500 104: ===================== Testing CoulombMat ======================= 104: CM test 1 mat Done - 97/208 Test #104: testCoulombMat ......................... Passed 0.13 sec + 97/208 Test #104: testCoulombMat ......................... Passed 0.05 sec test 105 Start 105: descriptorsTestCatch @@ -22547,25 +22525,90 @@ 105: =============================================================================== 105: All tests passed (130 assertions in 5 test cases) 105: - 98/208 Test #105: descriptorsTestCatch ................... Passed 0.34 sec + 98/208 Test #105: descriptorsTestCatch ................... Passed 0.06 sec test 106 Start 106: pyMolDescriptors 106: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 106: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 106: Test timeout computed to be: 1500 -97: =>start test 2 WHIM custom -97: [20:18:11] test on : 365 molecules done -103: =>start test autocorr3D -103: [20:18:12] test on : 365 molecules done - 99/208 Test #103: testAUTOCORR3D ......................... Passed 3.20 sec +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test Issue252: Bad definitions for Crippen atom types. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test calculation of ChiVs. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test calculation of ChiNs. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test calculation of HallKierAlpha. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test calculation of Kappa1. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test calculation of Kappa2. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test calculation of Kappa3. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test Crippen atom type calculations. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test ring descriptors +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test other count descriptors. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test MQN +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test GitHub Issue 56. +91: [07:09:40] WARNING: not removing hydrogen atom without neighbors +91: [07:09:40] WARNING: not removing hydrogen atom without neighbors +91: [07:09:40] WARNING: not removing hydrogen atom without neighbors +91: [07:09:40] WARNING: not removing hydrogen atom without neighbors +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test Github92: Bad Crippen atom type for pyrrole H. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test Github362: order dependence in Kier-Hall descriptors. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test calculation of spiro and bridgehead counts. +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test Github694: ExactMolWt ignoring the mass of the electron +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Testing Properties and KitchenSink +91: [07:09:40] ---Caught keyerror (bad property name)--- +91: [07:09:40] ---Caught stereo value error--- +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test USR Descriptor +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test Github #1973: support P and S terms for TPSA calculation +91: [07:09:40] done +91: [07:09:40] ------------------------------------- +91: [07:09:40] Test Github #2948: Empty molecule has non-zero LabuteASA +91: [07:09:40] done + 99/208 Test #91: testDescriptors ........................ Passed 8.61 sec test 107 Start 107: pyMolDescriptors3D 107: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Descriptors/Wrap/test3D.py" 107: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 107: Test timeout computed to be: 1500 -106: .....[20:18:14] +106: .....[07:09:40] 106: 106: **** 106: Pre-condition Violation @@ -22574,11 +22617,9 @@ 106: Failed Expression: atom_props.size() == num_atoms 106: **** 106: -97: =>start test 1 WHIM custom -97: [20:18:14] test on : 365 molecules done 106: ........................ 106: ---------------------------------------------------------------------- -106: Ran 29 tests in 0.312s +106: Ran 29 tests in 0.073s 106: 106: OK 106: exactmw 78.046950192 @@ -22626,12 +22667,7 @@ 106: Phi 0.9130327103921437 106: exactmw 78.046950192 106: lipinskiHBA 0.0 -107: ........ -107: ---------------------------------------------------------------------- -107: Ran 8 tests in 0.942s -107: -107: OK -100/208 Test #106: pyMolDescriptors ....................... Passed 4.02 sec +100/208 Test #106: pyMolDescriptors ....................... Passed 0.87 sec test 108 Start 108: testFingerprints @@ -23121,267 +23157,273 @@ 108: 108: ------------------- 108: -101/208 Test #107: pyMolDescriptors3D ..................... Passed 3.64 sec +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Morgan Fingerprints. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Morgan Fingerprints using fromAtoms argument. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Morgan Fingerprints as bit vects. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Morgan Fingerprints with feature invariants. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test additional Morgan fingerprints options. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Atom Codes. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Atom Pairs. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Atom Pairs part 2. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Topological Torsions. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Bulk Topological Torsions. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Hashed Atom Pairs. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Hashed torsions. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Rooted Atom Pairs. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test ignoring atoms in Atom Pairs. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Rooted Topological Torsions. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test ignoring atoms in Topological Torsions. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test atom info from morgan fingerprints. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test atom info from morgan fingerprints including Info Redundant Environments. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] ------------------------------------- +108: [07:09:40] ------------------------------------- +108: [07:09:40] ------------------------------------- +108: [07:09:40] ------------------------------------- +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Atom Pairs including info about chirality. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test Topological Torsions including info about chirality. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test GitHub Issue 25: fingerprint backwards compatibility. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test GitHub Issue 151: PatternFingerprint problems +107: ........ +107: ---------------------------------------------------------------------- +107: Ran 8 tests in 0.343s +107: +107: OK +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test 3D atom pairs. +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +108: [07:09:40] done +108: [07:09:40] ------------------------------------- +108: [07:09:40] Test multithreading with the pattern FP +108: reading molecules +108: pass 1 +108: launch :0 +108: launch :1 +108: launch :2 +108: launch :3 +101/208 Test #107: pyMolDescriptors3D ..................... Passed 1.02 sec test 109 Start 109: testMHFPFingerprint 109: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 109: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 109: Test timeout computed to be: 1500 -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Morgan Fingerprints. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Morgan Fingerprints using fromAtoms argument. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Morgan Fingerprints as bit vects. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Morgan Fingerprints with feature invariants. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test additional Morgan fingerprints options. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Atom Codes. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Atom Pairs. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Atom Pairs part 2. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Topological Torsions. -108: [20:18:15] done -108: [20:18:15] ------------------------------------- -108: [20:18:15] Test Bulk Topological Torsions. -109: [20:18:15] ------------------------------------- -109: [20:18:15] Test MHFP fingerprint encoder initialization -109: [20:18:15] done -109: [20:18:15] ------------------------------------- -109: [20:18:15] Test MHFP shingling creation -109: [20:18:16] done -109: [20:18:16] ------------------------------------- -109: [20:18:16] Test MHFP hashing of string and uint arrays -109: [20:18:16] done -109: [20:18:16] ------------------------------------- -109: [20:18:16] Test SECFP fingerprint functionality -109: [20:18:16] done -102/208 Test #109: testMHFPFingerprint .................... Passed 0.45 sec +109: [07:09:41] ------------------------------------- +109: [07:09:41] Test MHFP fingerprint encoder initialization +109: [07:09:41] done +109: [07:09:41] ------------------------------------- +109: [07:09:41] Test MHFP shingling creation +109: [07:09:41] done +109: [07:09:41] ------------------------------------- +109: [07:09:41] Test MHFP hashing of string and uint arrays +109: [07:09:41] done +109: [07:09:41] ------------------------------------- +109: [07:09:41] Test SECFP fingerprint functionality +109: [07:09:41] done +102/208 Test #109: testMHFPFingerprint .................... Passed 0.11 sec test 110 Start 110: testFingerprintGenerators 110: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 110: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 110: Test timeout computed to be: 1500 -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test atom-pair fp generator -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test atom-pair fp generator with different arguments -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test atom-pair additional output -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test Folded Atom Pairs. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test Rooted Atom Pairs. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test ignoring atoms in Atom Pairs. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test Atom Pairs including info about chirality. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test Morgan Fingerprints. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test morgan fp generator -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test Morgan Fingerprints using fromAtoms argument. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test Morgan Fingerprints as bit vects. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test Morgan Fingerprints with feature invariants. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test additional Morgan fingerprints options. -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Single atoms setting radius 1 bits in Morgan fingerprints -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test different invariant generator combinations -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test invariant overriding -110: [20:18:16] done -110: [20:18:16] ------------------------------------- -110: [20:18:16] Test RDKit fp generator -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test Hashed Atom Pairs. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test Hashed torsions. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test Rooted Atom Pairs. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test ignoring atoms in Atom Pairs. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test Rooted Topological Torsions. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test ignoring atoms in Topological Torsions. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test atom info from morgan fingerprints. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test atom info from morgan fingerprints including Info Redundant Environments. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] ------------------------------------- -108: [20:18:16] ------------------------------------- -108: [20:18:16] ------------------------------------- -108: [20:18:16] ------------------------------------- -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test Atom Pairs including info about chirality. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test Topological Torsions including info about chirality. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test GitHub Issue 25: fingerprint backwards compatibility. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test GitHub Issue 151: PatternFingerprint problems -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test 3D atom pairs. -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -108: [20:18:16] done -108: [20:18:16] ------------------------------------- -108: [20:18:16] Test multithreading with the pattern FP -108: reading molecules -108: pass 1 -108: launch :0 -108: launch :1 -108: launch :2 -108: launch :3 -108: pass 2 -108: launch :0 -108: launch :1 -108: launch :2 -108: launch :3 -110: [20:18:18] done -110: [20:18:18] ------------------------------------- -110: [20:18:18] Test unfolded version of RDKFP -110: [20:18:18] ------------------------------------- -110: [20:18:18] Test topological torsion fp generator -110: [20:18:18] done -110: [20:18:18] ------------------------------------- -110: [20:18:18] Test Topological Torsions. -110: [20:18:18] done -110: [20:18:18] ------------------------------------- -110: [20:18:18] Test Folded torsions. -110: [20:18:18] done -110: [20:18:18] ------------------------------------- -110: [20:18:18] Test Bulk Topological Torsions. +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test atom-pair fp generator +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test atom-pair fp generator with different arguments +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation 102: =>start test GETAWAY -102: [20:18:18] test on : 365 molecules done -103/208 Test #102: testGETAWAY ............................ Passed 12.46 sec +102: [07:09:41] test on : 365 molecules done +103/208 Test #102: testGETAWAY ............................ Passed 3.89 sec test 111 Start 111: fpTestCatch 111: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 111: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 111: Test timeout computed to be: 1500 +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test atom-pair additional output +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test Folded Atom Pairs. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test Rooted Atom Pairs. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test ignoring atoms in Atom Pairs. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test Atom Pairs including info about chirality. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test Morgan Fingerprints. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test morgan fp generator 111: =============================================================================== 111: All tests passed (163 assertions in 13 test cases) 111: -104/208 Test #111: fpTestCatch ............................ Passed 0.34 sec +104/208 Test #111: fpTestCatch ............................ Passed 0.06 sec test 112 Start 112: pyTestGenerator 112: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 112: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 112: Test timeout computed to be: 1500 -110: [20:18:19] done -110: [20:18:19] ------------------------------------- -110: [20:18:19] Test Rooted Topological Torsions. -110: [20:18:19] done -110: [20:18:19] ------------------------------------- -110: [20:18:19] Test ignoring atoms in Topological Torsions. -110: [20:18:19] done -110: [20:18:19] ------------------------------------- -110: [20:18:19] ------------------------------------- -110: [20:18:19] Test Topological Torsions including info about chirality. -110: [20:18:19] done -110: [20:18:19] ------------------------------------- -110: [20:18:19] Test GitHub Issue 25: fingerprint backwards compatibility. -110: [20:18:19] done -110: [20:18:19] ------------------------------------- -110: [20:18:19] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -110: [20:18:19] done -110: [20:18:19] ------------------------------------- -110: [20:18:19] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -110: [20:18:19] Warning: molecule is tagged as 3D, but all Z coords are zero -110: [20:18:19] done -110: [20:18:19] ------------------------------------- -110: [20:18:19] Test convenience and bulk fp calculation functions -112: ......... -112: ---------------------------------------------------------------------- -112: Ran 9 tests in 0.498s -112: -112: OK -110: [20:18:22] done -105/208 Test #110: testFingerprintGenerators .............. Passed 6.70 sec +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test Morgan Fingerprints using fromAtoms argument. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test Morgan Fingerprints as bit vects. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test Morgan Fingerprints with feature invariants. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test additional Morgan fingerprints options. +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Single atoms setting radius 1 bits in Morgan fingerprints +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test different invariant generator combinations +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test invariant overriding +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test RDKit fp generator +108: pass 2 +108: launch :0 +108: launch :1 +108: launch :2 +108: launch :3 +97: =>start test GETAWAY custom +97: [07:09:41] test on : 365 molecules done +105/208 Test #97: testRDFcustom .......................... Passed 7.25 sec test 113 Start 113: pyTestMHFP 113: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 113: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 113: Test timeout computed to be: 1500 -106/208 Test #112: pyTestGenerator ........................ Passed 4.38 sec +110: [07:09:41] done +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test unfolded version of RDKFP +110: [07:09:41] ------------------------------------- +110: [07:09:41] Test topological torsion fp generator +112: ......... +112: ---------------------------------------------------------------------- +112: Ran 9 tests in 0.075s +112: +112: OK +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test Topological Torsions. +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test Folded torsions. +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test Bulk Topological Torsions. +106/208 Test #112: pyTestGenerator ........................ Passed 0.70 sec test 114 Start 114: testPartialCharges 114: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 114: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 114: Test timeout computed to be: 1500 -107/208 Test #114: testPartialCharges ..................... Passed 0.23 sec +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test Rooted Topological Torsions. +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test ignoring atoms in Topological Torsions. +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +107/208 Test #114: testPartialCharges ..................... Passed 0.09 sec test 115 Start 115: pyPartialCharges 115: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 115: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 115: Test timeout computed to be: 1500 +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test Topological Torsions including info about chirality. +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test GitHub Issue 25: fingerprint backwards compatibility. +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +110: [07:09:42] Warning: molecule is tagged as 3D, but all Z coords are zero +110: [07:09:42] done +110: [07:09:42] ------------------------------------- +110: [07:09:42] Test convenience and bulk fp calculation functions 113: . 113: ---------------------------------------------------------------------- -113: Ran 1 test in 0.302s +113: Ran 1 test in 0.057s 113: 113: OK -108/208 Test #113: pyTestMHFP ............................. Passed 3.77 sec +108/208 Test #113: pyTestMHFP ............................. Passed 0.80 sec test 116 Start 116: testMolTransforms @@ -23418,61 +23460,69 @@ 116: testWeightedCentroid 116: 116: *********************************************************** -109/208 Test #116: testMolTransforms ...................... Passed 0.20 sec +109/208 Test #116: testMolTransforms ...................... Passed 0.06 sec test 117 Start 117: pyMolTransforms 117: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 117: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap 117: Test timeout computed to be: 1500 -97: =>start test GETAWAY custom -97: [20:18:28] test on : 365 molecules done -110/208 Test #97: testRDFcustom .......................... Passed 32.66 sec +110: [07:09:42] done +110/208 Test #110: testFingerprintGenerators .............. Passed 1.66 sec test 118 Start 118: testMMFFForceFieldHelpers 118: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 118: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 118: Test timeout computed to be: 1500 -118: [20:18:28] ------------------------------------- -118: [20:18:28] Test MMFF atom types. -118: [20:18:28] done -118: [20:18:28] ------------------------------------- -118: [20:18:28] Testing MMFF builder tools. -118: [20:18:28] done -118: [20:18:28] ------------------------------------- -118: [20:18:28] Testing MMFF builder+minimization. -115: ....... -115: ---------------------------------------------------------------------- -115: Ran 7 tests in 1.558s -115: -115: OK -118: [20:18:29] done -118: [20:18:29] ------------------------------------- -118: [20:18:29] Testing Issue239. -111/208 Test #115: pyPartialCharges ....................... Passed 5.61 sec +118: [07:09:42] ------------------------------------- +118: [07:09:42] Test MMFF atom types. +118: [07:09:42] done +118: [07:09:42] ------------------------------------- +118: [07:09:42] Testing MMFF builder tools. +118: [07:09:42] done +118: [07:09:42] ------------------------------------- +118: [07:09:42] Testing MMFF builder+minimization. +118: [07:09:43] done +118: [07:09:43] ------------------------------------- +118: [07:09:43] Testing Issue239. +118: [07:09:43] done +118: [07:09:43] ------------------------------------- +118: [07:09:43] Testing calcEnergy with passed coords. +118: [07:09:43] done +118: [07:09:43] ------------------------------------- +118: [07:09:43] Testing calcGrad. +118: [07:09:43] done +118: [07:09:43] ------------------------------------- +118: [07:09:43] Testing Issue242. +117: ........ +117: ---------------------------------------------------------------------- +117: Ran 8 tests in 0.062s +117: +117: OK +118: [07:09:43] done +118: [07:09:43] ------------------------------------- +118: [07:09:43] Testing github 308: crash during MMFF parameterization . +118: [07:09:43] ------------------------------------- +118: [07:09:43] Testing SFIssue1653802. +118: [07:09:43] done +118: [07:09:43] ------------------------------------- +118: [07:09:43] Testing SFIssue2378119. +118: [07:09:43] done +118: [07:09:43] ------------------------------------- +118: [07:09:43] Test MMFF force-field parameter getters. +118: [07:09:43] ------------------------------------- +118: [07:09:43] Test MMFF multithreading +118: generating reference data +111/208 Test #117: pyMolTransforms ........................ Passed 0.67 sec test 119 Start 119: testMMFFForceFieldHelpersMultiThread 119: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 119: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 119: Test timeout computed to be: 1500 -118: [20:18:29] done -118: [20:18:29] ------------------------------------- -118: [20:18:29] Testing calcEnergy with passed coords. -119: [20:18:29] ------------------------------------- -119: [20:18:29] Test MMFF multithreading -118: [20:18:29] done -118: [20:18:29] ------------------------------------- -118: [20:18:29] Testing calcGrad. -117: ........ -117: ---------------------------------------------------------------------- -117: Ran 8 tests in 0.485s -117: -117: OK -118: [20:18:30] done -118: [20:18:30] ------------------------------------- -118: [20:18:30] Testing Issue242. +119: [07:09:43] ------------------------------------- +119: [07:09:43] Test MMFF multithreading 119: processing 119: launch :0 119: launch :1 @@ -23498,660 +23548,618 @@ 119: launch :21 119: launch :22 119: launch :23 -118: [20:18:30] done -118: [20:18:30] ------------------------------------- -118: [20:18:30] Testing github 308: crash during MMFF parameterization . -118: [20:18:30] ------------------------------------- -118: [20:18:30] Testing SFIssue1653802. -118: [20:18:30] done -118: [20:18:30] ------------------------------------- -118: [20:18:30] Testing SFIssue2378119. -118: [20:18:30] done -118: [20:18:30] ------------------------------------- -118: [20:18:30] Test MMFF force-field parameter getters. -118: [20:18:30] ------------------------------------- -118: [20:18:30] Test MMFF multithreading -118: generating reference data -112/208 Test #117: pyMolTransforms ........................ Passed 4.10 sec +115: ....... +115: ---------------------------------------------------------------------- +115: Ran 7 tests in 0.507s +115: +115: OK +112/208 Test #115: pyPartialCharges ....................... Passed 1.96 sec test 120 Start 120: testUFFForceFieldHelpers 120: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 120: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF 120: Test timeout computed to be: 1500 -120: [20:18:31] ------------------------------------- -120: [20:18:31] Test UFF atom labels. -120: [20:18:31] done -120: [20:18:31] ------------------------------------- -120: [20:18:31] Test UFF atom typer. -120: [20:18:31] done -120: [20:18:31] ------------------------------------- -120: [20:18:31] Testing UFF builder tools. -120: [20:18:31] done -120: [20:18:31] ------------------------------------- -120: [20:18:31] Testing UFF builder+minimization. -120: [20:18:31] done -120: [20:18:31] ------------------------------------- -120: [20:18:31] Testing UFF special cases. -120: [20:18:31] UFFTYPER: Unrecognized charge state for atom: 0 -120: [20:18:31] done -120: [20:18:31] ------------------------------------- -120: [20:18:31] Testing Issue239. -120: [20:18:31] done -120: [20:18:31] ------------------------------------- -120: [20:18:31] Testing calcEnergy with passed coords. -120: [20:18:32] done -120: [20:18:32] ------------------------------------- -120: [20:18:32] Testing calcGrad. +120: [07:09:44] ------------------------------------- +120: [07:09:44] Test UFF atom labels. +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Test UFF atom typer. 119: done -120: [20:18:32] done -120: [20:18:32] ------------------------------------- -120: [20:18:32] Testing SFIssue1653802. -120: [20:18:32] done -120: [20:18:32] ------------------------------------- -120: [20:18:32] Testing SFIssue2378119. -120: [20:18:32] done -120: [20:18:32] ------------------------------------- -120: [20:18:32] Test UFF force-field parameter getters. -120: [20:18:32] ------------------------------------- -120: [20:18:32] Testing handling missing parameters. -120: [20:18:32] UFFTYPER: Unrecognized hybridization for atom: 0 -120: [20:18:32] UFFTYPER: Unrecognized atom type: Cu+1 (0) -119: [20:18:32] done -120: [20:18:32] UFFTYPER: Unrecognized hybridization for atom: 0 -120: [20:18:32] UFFTYPER: Unrecognized atom type: Cu+1 (0) -120: [20:18:32] done -120: [20:18:32] ------------------------------------- -120: [20:18:32] Testing SFIssue3009337. -120: [20:18:32] done -120: [20:18:32] ------------------------------------- -120: [20:18:32] Test UFF multithreading -113/208 Test #119: testMMFFForceFieldHelpersMultiThread ... Passed 2.66 sec +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing UFF builder tools. +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing UFF builder+minimization. +119: [07:09:44] done +113/208 Test #119: testMMFFForceFieldHelpersMultiThread ... Passed 1.11 sec test 121 Start 121: testCrystalForceField 121: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 121: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 121: Test timeout computed to be: 1500 -120: generating reference data +118: processing +118: launch :0 +118: launch :1 +118: launch :2 +118: launch :3 +118: [07:09:44] Rep: 0 Mol:0 121: ------------------------------------- 121: Test CrystalFF torsional term. -114/208 Test #121: testCrystalForceField .................. Passed 1.01 sec +118: [07:09:44] Rep: 0 Mol:3 +118: [07:09:44] Rep: 0 Mol:1 +118: [07:09:44] Rep: 0 Mol:4 +118: [07:09:44] Rep: 0 Mol:2 +118: [07:09:44] Rep: 0 Mol:5 +118: [07:09:44] Rep: 0 Mol:8 +118: [07:09:44] Rep: 0 Mol:9 +118: [07:09:44] Rep: 0 Mol:12 +118: [07:09:44] Rep: 0 Mol:16 +118: [07:09:44] Rep: 0 Mol:13 +118: [07:09:44] Rep: 0 Mol:20 +118: [07:09:44] Rep: 0 Mol:24 +118: [07:09:44] Rep: 0 Mol:28 +118: [07:09:44] Rep: 0 Mol:6 +118: [07:09:44] Rep: 0 Mol:17 +118: [07:09:44] Rep: 0 Mol:10 +118: [07:09:44] Rep: 0 Mol:7 +118: [07:09:44] Rep: 0 Mol:11 +118: [07:09:44] Rep: 0 Mol:15 +118: [07:09:44] Rep: 0 Mol:19 +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing UFF special cases. +120: [07:09:44] UFFTYPER: Unrecognized charge state for atom: 0 +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing Issue239. +118: [07:09:44] Rep: 0 Mol:23 +118: [07:09:44] Rep: 0 Mol:27 +118: [07:09:44] Rep: 0 Mol:31 +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing calcEnergy with passed coords. +118: [07:09:44] Rep: 0 Mol:21 +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing calcGrad. +118: [07:09:44] Rep: 0 Mol:25 +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing SFIssue1653802. +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing SFIssue2378119. +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Test UFF force-field parameter getters. +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing handling missing parameters. +120: [07:09:44] UFFTYPER: Unrecognized hybridization for atom: 0 +120: [07:09:44] UFFTYPER: Unrecognized atom type: Cu+1 (0) +120: [07:09:44] UFFTYPER: Unrecognized hybridization for atom: 0 +120: [07:09:44] UFFTYPER: Unrecognized atom type: Cu+1 (0) +118: [07:09:44] Rep: 0 Mol:29 +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Testing SFIssue3009337. +120: [07:09:44] done +120: [07:09:44] ------------------------------------- +120: [07:09:44] Test UFF multithreading +120: generating reference data +118: [07:09:45] Rep: 0 Mol:14 +118: [07:09:45] Rep: 0 Mol:18 +118: [07:09:45] Rep: 0 Mol:22 +118: [07:09:45] Rep: 0 Mol:26 +114/208 Test #121: testCrystalForceField .................. Passed 0.77 sec test 122 Start 122: pyForceFieldHelpers 122: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 122: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 122: Test timeout computed to be: 1500 +118: [07:09:45] Rep: 0 Mol:30 +118: [07:09:45] Rep: 20 Mol:3 +118: [07:09:45] Rep: 20 Mol:7 +118: [07:09:45] Rep: 20 Mol:11 +118: [07:09:45] Rep: 20 Mol:15 +118: [07:09:45] Rep: 20 Mol:19 +118: [07:09:45] Rep: 20 Mol:23 +118: [07:09:45] Rep: 20 Mol:27 +118: [07:09:45] Rep: 20 Mol:31 +118: [07:09:45] Rep: 20 Mol:0 +118: [07:09:45] Rep: 20 Mol:4 +118: [07:09:45] Rep: 20 Mol:8 +118: [07:09:45] Rep: 20 Mol:12 +118: [07:09:45] Rep: 20 Mol:16 +118: [07:09:45] Rep: 20 Mol:20 +118: [07:09:45] Rep: 20 Mol:24 +118: [07:09:45] Rep: 20 Mol:28 +118: [07:09:45] Rep: 40 Mol:3 +118: [07:09:45] Rep: 40 Mol:7 +118: [07:09:45] Rep: 40 Mol:11 +118: [07:09:45] Rep: 40 Mol:15 +118: [07:09:45] Rep: 40 Mol:19 +118: [07:09:45] Rep: 40 Mol:23 +118: [07:09:45] Rep: 40 Mol:27 +118: [07:09:45] Rep: 40 Mol:31 120: processing 120: launch :0 120: launch :1 120: launch :2 120: launch :3 -120: [20:18:34] Rep: 0 Mol:2 -120: [20:18:34] Rep: 0 Mol:3 -120: [20:18:34] Rep: 0 Mol:1 -120: [20:18:34] Rep: 0 Mol:0 -120: [20:18:34] Rep: 0 Mol:5 -120: [20:18:34] Rep: 0 Mol:9 -120: [20:18:34] Rep: 0 Mol:4 -120: [20:18:34] Rep: 0 Mol:13 -122: [20:18:34] Molecule does not have explicit Hs. Consider calling AddHs() -120: [20:18:34] Rep: 0 Mol:6 -120: [20:18:34] Rep: 0 Mol:7 -120: [20:18:34] Rep: 0 Mol:11 -122: [20:18:34] Molecule does not have explicit Hs. Consider calling AddHs() -122: [20:18:34] Molecule does not have explicit Hs. Consider calling AddHs() -122: [20:18:34] Molecule does not have explicit Hs. Consider calling AddHs() -122: [20:18:34] Molecule does not have explicit Hs. Consider calling AddHs() -122: ..[20:18:35] Molecule does not have explicit Hs. Consider calling AddHs() -120: [20:18:35] Rep: 0 Mol:17 -122: [20:18:35] Molecule does not have explicit Hs. Consider calling AddHs() -120: [20:18:35] Rep: 0 Mol:10 -120: [20:18:35] Rep: 0 Mol:15 -122: .[20:18:35] Molecule does not have explicit Hs. Consider calling AddHs() -120: [20:18:35] Rep: 0 Mol:19 -120: [20:18:35] Rep: 0 Mol:23 -120: [20:18:35] Rep: 0 Mol:27 -120: [20:18:35] Rep: 0 Mol:8 -120: [20:18:35] Rep: 0 Mol:12 -120: [20:18:35] Rep: 0 Mol:31 -120: [20:18:35] Rep: 0 Mol:16 -122: .[20:18:35] Molecule does not have explicit Hs. Consider calling AddHs() -120: [20:18:35] Rep: 0 Mol:21 -120: [20:18:35] Rep: 0 Mol:14 -120: [20:18:35] Rep: 0 Mol:20 -120: [20:18:35] Rep: 0 Mol:25 -120: [20:18:35] Rep: 0 Mol:24 -120: [20:18:35] Rep: 0 Mol:18 -120: [20:18:35] Rep: 0 Mol:29 -120: [20:18:35] Rep: 0 Mol:28 -120: [20:18:35] Rep: 0 Mol:22 -120: [20:18:35] Rep: 0 Mol:26 -120: [20:18:35] Rep: 0 Mol:30 -122: .[20:18:35] Molecule does not have explicit Hs. Consider calling AddHs() -118: processing -118: launch :0 -118: launch :1 -118: launch :2 -118: launch :3 -118: [20:18:36] Rep: 0 Mol:0 -118: [20:18:36] Rep: 0 Mol:2 -118: [20:18:36] Rep: 0 Mol:3 -118: [20:18:36] Rep: 0 Mol:1 -122: .[20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -118: [20:18:36] Rep: 0 Mol:5 -118: [20:18:36] Rep: 0 Mol:9 -118: [20:18:36] Rep: 0 Mol:4 -118: [20:18:36] Rep: 0 Mol:13 -118: [20:18:36] Rep: 0 Mol:17 -122: .[20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[20:18:36] UFFTYPER: Unrecognized hybridization for atom: 0 -122: [20:18:36] UFFTYPER: Unrecognized atom type: Cu+1 (0) -118: [20:18:36] Rep: 0 Mol:6 -118: [20:18:36] Rep: 0 Mol:8 -122: .[20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: [20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: [20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -118: [20:18:36] Rep: 0 Mol:10 -122: [20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: [20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: .[20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: [20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: ..[20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -122: [20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -118: [20:18:36] Rep: 0 Mol:12 -118: [20:18:36] Rep: 0 Mol:16 -118: [20:18:36] Rep: 0 Mol:7 -118: [20:18:36] Rep: 0 Mol:11 -118: [20:18:36] Rep: 0 Mol:20 -118: [20:18:36] Rep: 0 Mol:15 -118: [20:18:36] Rep: 0 Mol:21 -118: [20:18:36] Rep: 0 Mol:24 -122: [20:18:36] Molecule does not have explicit Hs. Consider calling AddHs() -118: [20:18:36] Rep: 0 Mol:19 -118: [20:18:36] Rep: 0 Mol:28 -118: [20:18:36] Rep: 0 Mol:25 -118: [20:18:36] Rep: 0 Mol:23 -118: [20:18:36] Rep: 0 Mol:27 -118: [20:18:37] Rep: 0 Mol:31 -118: [20:18:37] Rep: 0 Mol:29 +120: [07:09:45] Rep: 0 Mol:2 +120: [07:09:45] Rep: 0 Mol:0 +120: [07:09:45] Rep: 0 Mol:1 +120: [07:09:45] Rep: 0 Mol:3 +120: [07:09:45] Rep: 0 Mol:5 +120: [07:09:45] Rep: 0 Mol:9 +120: [07:09:45] Rep: 0 Mol:4 +120: [07:09:45] Rep: 0 Mol:13 +120: [07:09:45] Rep: 0 Mol:6 +120: [07:09:46] Rep: 0 Mol:17 +120: [07:09:46] Rep: 0 Mol:10 +120: [07:09:46] Rep: 0 Mol:8 +120: [07:09:46] Rep: 0 Mol:7 +120: [07:09:46] Rep: 0 Mol:11 +120: [07:09:46] Rep: 0 Mol:12 +120: [07:09:46] Rep: 0 Mol:16 +120: [07:09:46] Rep: 0 Mol:15 +120: [07:09:46] Rep: 0 Mol:21 +120: [07:09:46] Rep: 0 Mol:19 +120: [07:09:46] Rep: 0 Mol:20 +118: [07:09:46] Rep: 20 Mol:1 +118: [07:09:46] Rep: 20 Mol:5 +118: [07:09:46] Rep: 20 Mol:9 +120: [07:09:46] Rep: 0 Mol:14 +120: [07:09:46] Rep: 0 Mol:25 +120: [07:09:46] Rep: 0 Mol:23 +120: [07:09:46] Rep: 0 Mol:27 +118: [07:09:46] Rep: 20 Mol:13 +118: [07:09:46] Rep: 20 Mol:17 +120: [07:09:46] Rep: 0 Mol:24 +120: [07:09:46] Rep: 0 Mol:18 +120: [07:09:46] Rep: 0 Mol:29 +120: [07:09:46] Rep: 0 Mol:28 +118: [07:09:46] Rep: 20 Mol:21 +118: [07:09:46] Rep: 20 Mol:25 +120: [07:09:46] Rep: 0 Mol:31 +118: [07:09:46] Rep: 20 Mol:29 +120: [07:09:46] Rep: 0 Mol:22 +120: [07:09:46] Rep: 0 Mol:26 +120: [07:09:46] Rep: 0 Mol:30 +118: [07:09:46] Rep: 40 Mol:0 +118: [07:09:46] Rep: 40 Mol:4 +118: [07:09:46] Rep: 40 Mol:8 +118: [07:09:46] Rep: 60 Mol:3 +118: [07:09:46] Rep: 60 Mol:7 +118: [07:09:46] Rep: 60 Mol:11 +118: [07:09:46] Rep: 40 Mol:12 +118: [07:09:46] Rep: 40 Mol:16 +118: [07:09:46] Rep: 40 Mol:20 +118: [07:09:46] Rep: 40 Mol:24 +118: [07:09:46] Rep: 40 Mol:28 +118: [07:09:46] Rep: 60 Mol:15 +118: [07:09:46] Rep: 60 Mol:19 +118: [07:09:46] Rep: 60 Mol:23 +118: [07:09:46] Rep: 60 Mol:27 +118: [07:09:46] Rep: 60 Mol:31 +118: [07:09:46] Rep: 20 Mol:2 +118: [07:09:46] Rep: 20 Mol:6 +118: [07:09:46] Rep: 20 Mol:10 +118: [07:09:46] Rep: 20 Mol:14 +118: [07:09:46] Rep: 20 Mol:18 +118: [07:09:46] Rep: 20 Mol:22 +118: [07:09:46] Rep: 20 Mol:26 +118: [07:09:46] Rep: 20 Mol:30 +122: [07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: ..[07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[07:09:46] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +118: [07:09:47] Rep: 80 Mol:3 +118: [07:09:47] Rep: 80 Mol:7 +118: [07:09:47] Rep: 80 Mol:11 +118: [07:09:47] Rep: 80 Mol:15 +118: [07:09:47] Rep: 80 Mol:19 +118: [07:09:47] Rep: 80 Mol:23 +118: [07:09:47] Rep: 80 Mol:27 +118: [07:09:47] Rep: 80 Mol:31 +122: .[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +118: [07:09:47] Rep: 40 Mol:1 +118: [07:09:47] Rep: 40 Mol:5 +118: [07:09:47] Rep: 40 Mol:9 +118: [07:09:47] Rep: 40 Mol:13 +118: [07:09:47] Rep: 40 Mol:17 +118: [07:09:47] Rep: 40 Mol:21 +118: [07:09:47] Rep: 40 Mol:25 +118: [07:09:47] Rep: 40 Mol:29 +122: .[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[07:09:47] UFFTYPER: Unrecognized hybridization for atom: 0 +122: [07:09:47] UFFTYPER: Unrecognized atom type: Cu+1 (0) +122: .[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +118: [07:09:47] Rep: 60 Mol:0 +118: [07:09:47] Rep: 60 Mol:4 +122: [07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +118: [07:09:47] Rep: 60 Mol:8 +118: [07:09:47] Rep: 60 Mol:12 +118: [07:09:47] Rep: 60 Mol:16 +122: .[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: .[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: ..[07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +122: [07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +118: [07:09:47] Rep: 60 Mol:20 +118: [07:09:47] Rep: 60 Mol:24 +118: [07:09:47] Rep: 60 Mol:28 +122: [07:09:47] Molecule does not have explicit Hs. Consider calling AddHs() +118: [07:09:47] Rep: 40 Mol:2 +118: [07:09:47] Rep: 40 Mol:6 +118: [07:09:47] Rep: 40 Mol:10 +118: [07:09:47] Rep: 40 Mol:14 +118: [07:09:47] Rep: 40 Mol:18 +118: [07:09:47] Rep: 40 Mol:22 +118: [07:09:47] Rep: 40 Mol:26 +118: [07:09:47] Rep: 40 Mol:30 122: ... 122: ---------------------------------------------------------------------- -122: Ran 18 tests in 2.482s +122: Ran 18 tests in 0.813s 122: 122: OK -118: [20:18:37] Rep: 0 Mol:14 -118: [20:18:37] Rep: 0 Mol:18 -118: [20:18:37] Rep: 0 Mol:22 -118: [20:18:37] Rep: 20 Mol:0 -118: [20:18:37] Rep: 20 Mol:4 -118: [20:18:37] Rep: 20 Mol:8 -118: [20:18:37] Rep: 20 Mol:12 -118: [20:18:37] Rep: 20 Mol:16 -118: [20:18:37] Rep: 20 Mol:20 -118: [20:18:38] Rep: 20 Mol:24 -118: [20:18:38] Rep: 20 Mol:28 -118: [20:18:38] Rep: 0 Mol:26 -115/208 Test #122: pyForceFieldHelpers .................... Passed 5.13 sec +115/208 Test #122: pyForceFieldHelpers .................... Passed 2.64 sec test 123 Start 123: testDistGeomHelpers 123: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 123: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 123: Test timeout computed to be: 1500 -118: [20:18:38] Rep: 0 Mol:30 +25: Checking against /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 123: go 123: ------------------------------------- 123: -118: [20:18:38] Rep: 20 Mol:3 -118: [20:18:38] Rep: 20 Mol:7 -118: [20:18:38] Rep: 20 Mol:11 -118: [20:18:38] Rep: 20 Mol:15 -118: [20:18:38] Rep: 20 Mol:19 -118: [20:18:38] Rep: 20 Mol:23 -118: [20:18:38] Rep: 20 Mol:27 -118: [20:18:38] Rep: 20 Mol:31 -118: [20:18:39] Rep: 20 Mol:1 -118: [20:18:39] Rep: 20 Mol:5 -118: [20:18:39] Rep: 20 Mol:9 -118: [20:18:39] Rep: 20 Mol:13 -118: [20:18:39] Rep: 20 Mol:17 -118: [20:18:39] Rep: 20 Mol:21 -118: [20:18:39] Rep: 20 Mol:25 -118: [20:18:39] Rep: 20 Mol:29 -118: [20:18:40] Rep: 20 Mol:2 -118: [20:18:40] Rep: 20 Mol:6 -118: [20:18:40] Rep: 20 Mol:10 -118: [20:18:40] Rep: 20 Mol:14 -118: [20:18:40] Rep: 20 Mol:18 -118: [20:18:40] Rep: 20 Mol:22 -118: [20:18:40] Rep: 20 Mol:26 -118: [20:18:40] Rep: 20 Mol:30 -118: [20:18:40] Rep: 40 Mol:3 -118: [20:18:40] Rep: 40 Mol:7 -118: [20:18:40] Rep: 40 Mol:11 -118: [20:18:40] Rep: 40 Mol:15 -118: [20:18:40] Rep: 40 Mol:19 -118: [20:18:40] Rep: 40 Mol:23 -118: [20:18:40] Rep: 40 Mol:27 -120: [20:18:40] Rep: 100 Mol:3 -120: [20:18:40] Rep: 100 Mol:7 -118: [20:18:40] Rep: 40 Mol:31 -118: [20:18:40] Rep: 40 Mol:0 -118: [20:18:40] Rep: 40 Mol:4 -120: [20:18:40] Rep: 100 Mol:11 -120: [20:18:40] Rep: 100 Mol:15 -120: [20:18:40] Rep: 100 Mol:19 -120: [20:18:40] Rep: 100 Mol:23 -120: [20:18:40] Rep: 100 Mol:27 -120: [20:18:40] Rep: 100 Mol:31 -118: [20:18:40] Rep: 40 Mol:8 -118: [20:18:40] Rep: 40 Mol:12 -118: [20:18:40] Rep: 40 Mol:16 -118: [20:18:40] Rep: 40 Mol:20 -118: [20:18:40] Rep: 40 Mol:24 -118: [20:18:40] Rep: 40 Mol:28 -118: [20:18:41] Rep: 40 Mol:1 -118: [20:18:41] Rep: 40 Mol:5 -118: [20:18:41] Rep: 40 Mol:9 -118: [20:18:41] Rep: 40 Mol:13 -120: [20:18:41] Rep: 100 Mol:0 -118: [20:18:41] Rep: 60 Mol:3 -120: [20:18:41] Rep: 100 Mol:4 -118: [20:18:41] Rep: 60 Mol:7 -118: [20:18:41] Rep: 60 Mol:11 -120: [20:18:41] Rep: 100 Mol:8 -120: [20:18:41] Rep: 100 Mol:12 -120: [20:18:41] Rep: 100 Mol:16 -118: [20:18:41] Rep: 60 Mol:15 -118: [20:18:41] Rep: 60 Mol:19 -118: [20:18:41] Rep: 60 Mol:23 -118: [20:18:41] Rep: 60 Mol:27 -118: [20:18:41] Rep: 60 Mol:31 -120: [20:18:41] Rep: 100 Mol:20 -120: [20:18:41] Rep: 100 Mol:24 -120: [20:18:41] Rep: 100 Mol:28 -120: [20:18:41] Rep: 100 Mol:1 -120: [20:18:41] Rep: 100 Mol:5 -120: [20:18:41] Rep: 100 Mol:9 -118: [20:18:41] Rep: 40 Mol:17 -120: [20:18:41] Rep: 100 Mol:13 -120: [20:18:41] Rep: 100 Mol:17 -120: [20:18:41] Rep: 100 Mol:21 -120: [20:18:41] Rep: 100 Mol:25 -120: [20:18:41] Rep: 100 Mol:29 -118: [20:18:41] Rep: 40 Mol:21 -118: [20:18:41] Rep: 40 Mol:25 -118: [20:18:41] Rep: 40 Mol:29 -118: [20:18:42] Rep: 60 Mol:0 -118: [20:18:42] Rep: 60 Mol:4 -118: [20:18:42] Rep: 60 Mol:8 -118: [20:18:42] Rep: 60 Mol:12 -118: [20:18:42] Rep: 60 Mol:16 -118: [20:18:42] Rep: 60 Mol:20 -118: [20:18:42] Rep: 60 Mol:24 -118: [20:18:42] Rep: 60 Mol:28 -118: [20:18:42] Rep: 40 Mol:2 -118: [20:18:42] Rep: 40 Mol:6 -118: [20:18:42] Rep: 40 Mol:10 -118: [20:18:42] Rep: 40 Mol:14 -118: [20:18:42] Rep: 40 Mol:18 -118: [20:18:42] Rep: 40 Mol:22 -118: [20:18:42] Rep: 40 Mol:26 -118: [20:18:42] Rep: 40 Mol:30 -118: [20:18:43] Rep: 80 Mol:3 -118: [20:18:43] Rep: 80 Mol:7 -118: [20:18:43] Rep: 80 Mol:11 -118: [20:18:43] Rep: 80 Mol:15 -118: [20:18:43] Rep: 80 Mol:19 -118: [20:18:43] Rep: 80 Mol:23 -118: [20:18:43] Rep: 80 Mol:27 -118: [20:18:43] Rep: 80 Mol:31 -118: [20:18:43] Rep: 60 Mol:1 -118: [20:18:43] Rep: 60 Mol:5 -118: [20:18:43] Rep: 60 Mol:9 -118: [20:18:43] Rep: 60 Mol:13 -118: [20:18:43] Rep: 60 Mol:17 -118: [20:18:43] Rep: 60 Mol:21 -118: [20:18:43] Rep: 60 Mol:25 -118: [20:18:43] Rep: 60 Mol:29 -120: [20:18:43] Rep: 100 Mol:2 -120: [20:18:43] Rep: 100 Mol:6 -120: [20:18:43] Rep: 100 Mol:10 -120: [20:18:43] Rep: 100 Mol:14 -120: [20:18:43] Rep: 100 Mol:18 -120: [20:18:44] Rep: 100 Mol:22 -120: [20:18:44] Rep: 100 Mol:26 -120: [20:18:44] Rep: 100 Mol:30 -118: [20:18:44] Rep: 80 Mol:0 -118: [20:18:44] Rep: 80 Mol:4 -118: [20:18:44] Rep: 80 Mol:8 -118: [20:18:44] Rep: 80 Mol:12 -118: [20:18:44] Rep: 80 Mol:16 -118: [20:18:44] Rep: 80 Mol:20 -118: [20:18:44] Rep: 80 Mol:24 -118: [20:18:44] Rep: 80 Mol:28 -118: [20:18:45] Rep: 60 Mol:2 -118: [20:18:45] Rep: 60 Mol:6 -118: [20:18:45] Rep: 60 Mol:10 -118: [20:18:45] Rep: 60 Mol:14 -118: [20:18:45] Rep: 60 Mol:18 -118: [20:18:45] Rep: 60 Mol:22 -118: [20:18:45] Rep: 60 Mol:26 -118: [20:18:45] Rep: 60 Mol:30 -118: [20:18:45] Rep: 80 Mol:1 -118: [20:18:45] Rep: 80 Mol:5 -118: [20:18:45] Rep: 80 Mol:9 -118: [20:18:45] Rep: 80 Mol:13 -118: [20:18:45] Rep: 80 Mol:17 -118: [20:18:45] Rep: 80 Mol:21 -118: [20:18:45] Rep: 80 Mol:25 -118: [20:18:45] Rep: 80 Mol:29 -118: [20:18:47] Rep: 80 Mol:2 -118: [20:18:47] Rep: 80 Mol:6 -118: [20:18:47] Rep: 80 Mol:10 -118: [20:18:47] Rep: 80 Mol:14 -118: [20:18:47] Rep: 80 Mol:18 -118: [20:18:47] Rep: 80 Mol:22 -118: [20:18:47] Rep: 80 Mol:26 -118: [20:18:47] Rep: 80 Mol:30 -118: [20:18:48] done -118: [20:18:48] ------------------------------------- -118: [20:18:48] Test MMFF multithreading2 -120: [20:18:50] done -120: [20:18:50] ------------------------------------- -120: [20:18:50] Test UFF multithreading2 +120: [07:09:48] Rep: 100 Mol:1 +120: [07:09:48] Rep: 100 Mol:5 +120: [07:09:48] Rep: 100 Mol:9 +120: [07:09:48] Rep: 100 Mol:13 +120: [07:09:48] Rep: 100 Mol:17 +120: [07:09:48] Rep: 100 Mol:21 +120: [07:09:48] Rep: 100 Mol:25 +120: [07:09:48] Rep: 100 Mol:29 +120: [07:09:48] Rep: 100 Mol:3 +118: [07:09:48] Rep: 60 Mol:1 +118: [07:09:48] Rep: 60 Mol:5 +118: [07:09:48] Rep: 60 Mol:9 +118: [07:09:48] Rep: 60 Mol:13 +120: [07:09:48] Rep: 100 Mol:7 +120: [07:09:48] Rep: 100 Mol:11 +120: [07:09:48] Rep: 100 Mol:15 +120: [07:09:48] Rep: 100 Mol:19 +120: [07:09:48] Rep: 100 Mol:23 +120: [07:09:48] Rep: 100 Mol:27 +120: [07:09:48] Rep: 100 Mol:31 +118: [07:09:48] Rep: 60 Mol:17 +118: [07:09:48] Rep: 60 Mol:21 +118: [07:09:48] Rep: 60 Mol:25 +118: [07:09:48] Rep: 60 Mol:29 +120: [07:09:48] Rep: 100 Mol:0 +120: [07:09:48] Rep: 100 Mol:4 +120: [07:09:48] Rep: 100 Mol:8 +120: [07:09:48] Rep: 100 Mol:12 +120: [07:09:48] Rep: 100 Mol:16 +120: [07:09:48] Rep: 100 Mol:20 +120: [07:09:48] Rep: 100 Mol:24 +120: [07:09:48] Rep: 100 Mol:28 +118: [07:09:48] Rep: 80 Mol:0 +118: [07:09:48] Rep: 80 Mol:4 +118: [07:09:48] Rep: 80 Mol:8 +118: [07:09:48] Rep: 80 Mol:12 +118: [07:09:48] Rep: 80 Mol:16 +118: [07:09:48] Rep: 80 Mol:20 +118: [07:09:48] Rep: 80 Mol:24 +25: All 191 tests passed +25: done +25: ------------------------------------- +25: Unit tests for all MMFF constraint terms. +118: [07:09:48] Rep: 80 Mol:28 +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. 76: 0,0 0 76: 0,1 0 76: 1,0 0 76: 1,1 0 76: 2,0 0 76: 2,1 0 -116/208 Test #76: testEnumeration ........................ Passed 91.87 sec +116/208 Test #76: testEnumeration ........................ Passed 24.63 sec test 124 Start 124: distGeomHelpersCatch 124: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 124: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 124: Test timeout computed to be: 1500 -108: [20:18:51] done -108: [20:18:51] ------------------------------------- -108: [20:18:51] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -108: [20:18:52] Warning: molecule is tagged as 3D, but all Z coords are zero -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Test unfolded version of RDKFP -108: [20:18:52] ------------------------------------- -108: [20:18:52] Test bitinfo of RDKFP -108: [20:18:52] ------------------------------------- -108: [20:18:52] Single atoms setting radius 1 bits in Morgan fingerprints -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Github #879: Pattern fingerprint should set bits for single-atom fragments. -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Github #2115: BitInfo not complete for RDKFingerprint -108: [20:18:52] done -108: [20:18:52] ------------------------------------- -108: [20:18:52] Github #3723: Fingerprint crash for mols with Zero order bonds -117/208 Test #108: testFingerprints ....................... Passed 36.90 sec +118: [07:09:48] Rep: 60 Mol:2 +118: [07:09:48] Rep: 60 Mol:6 +118: [07:09:48] Rep: 60 Mol:10 +118: [07:09:48] Rep: 60 Mol:14 +118: [07:09:48] Rep: 60 Mol:18 +118: [07:09:48] Rep: 60 Mol:22 +118: [07:09:48] Rep: 60 Mol:26 +118: [07:09:48] Rep: 60 Mol:30 +124: [07:09:48] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, (0, 100, 0, 0, 0, 0) +124: [07:09:48] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, (0, 0, 2.5, 0, 0, 0) +124: [07:09:48] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, (0, 0, 4, 0, 0, 0) +124: [07:09:48] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, (0, 0, 4, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, (0, 0, 4, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, (0, 0, 4, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, (0, 0, 4, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, (0, 0, 4, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, (0, 0, 4, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, (0, 0, 7, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, (0, 0, 7, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, (0, 0, 7, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, (0, 0, 7, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, (0, 0, 7, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, (0, 0, 7, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, (0, 0, 7, 0, 0, 0) +124: [07:09:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, (0, 0, 7, 0, 0, 0) +124: [07:09:48] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, (-1, -0.5, -0.2, -0.3, 0, -0.3) +124: [07:09:49] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, (0, 3.6, 0, 0, 0, 0) +124: [07:09:49] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, (0, 100, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, (0, 0, 4, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, (100, 0, 0, 0, 0, 0) +124: [07:09:49] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, (0, 0, 1, 0, 0, 0) +124: [07:09:49] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, (0, 0, 1, 0, 0, 0) +124: [07:09:49] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, (0, 0, 1, 0, 0, 0) +124: [07:09:49] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, (0, 0, 1, 0, 0, 0) +124: [07:09:49] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, (0, 10, 0, 0, 0, 0) +124: [07:09:49] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, (0, 0, 4, 0, 0, 0) +124: [07:09:49] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, (0, 0, 4, 0, 0, 0) +124: [07:09:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, (0, 3, 0, 0, 0, 0) +124: [07:09:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, (0, 3, 0, 0, 0, 0) +124: [07:09:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, (0, 3, 0, 0, 0, 0) +124: [07:09:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, (0, 3, 0, 0, 0, 0) +124: [07:09:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, (0, 3, 0, 0, 0, 0) +124: [07:09:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, (0, 3, 0, 0, 0, 0) +124: [07:09:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, (0, 3, 0, 0, 0, 0) +124: [07:09:49] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, (0, 3, 0, 0, 0, 0) +124: ----------- +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, (0, 0, 4, 0, 0, 0) +124: [07:09:49] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, (0, 0, 4, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, (100, 0, 0, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, (100, 0, 0, 0, 0, 0) +124: [07:09:49] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, (0, 10, 0, 0, 0, 0) +124: [07:09:49] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, (0, 10, 0, 0, 0, 0) +124: [07:09:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, (0, 0, 1, 0, 0, 0) +124: [07:09:49] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, (0, 0, 1, 0, 0, 0) +124: ----------- +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, (0, 0, 4, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, (100, 0, 0, 0, 0, 0) +124: [07:09:49] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, (0, 10, 0, 0, 0, 0) +124: ----------- +124: ----------- +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, (0, 8, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, (5, 0, 0, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, (0, 0, 2, 0, 0, 0) +124: [07:09:49] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, (0, 0, 2, 0, 0, 0) +118: [07:09:49] Rep: 80 Mol:1 +118: [07:09:49] Rep: 80 Mol:5 +118: [07:09:49] Rep: 80 Mol:9 +118: [07:09:49] Rep: 80 Mol:13 +118: [07:09:49] Rep: 80 Mol:17 +118: [07:09:49] Rep: 80 Mol:21 +118: [07:09:49] Rep: 80 Mol:25 +118: [07:09:49] Rep: 80 Mol:29 +25: done +117/208 Test #25: testMMFFForceField ..................... Passed 33.19 sec test 125 Start 125: pyDistGeomHelpers 125: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 125: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 125: Test timeout computed to be: 1500 -124: [20:18:52] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, (0, 100, 0, 0, 0, 0) -124: [20:18:52] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, (0, 0, 2.5, 0, 0, 0) -124: [20:18:52] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, (0, 0, 7, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, (0, 0, 7, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, (0, 0, 7, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, (0, 0, 7, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, (0, 0, 7, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, (0, 0, 7, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, (0, 0, 7, 0, 0, 0) -124: [20:18:52] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, (0, 0, 7, 0, 0, 0) -124: [20:18:52] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, (-1, -0.5, -0.2, -0.3, 0, -0.3) -124: [20:18:52] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, (0, 3.6, 0, 0, 0, 0) -124: [20:18:52] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, (0, 100, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, (100, 0, 0, 0, 0, 0) -124: [20:18:52] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, (0, 0, 1, 0, 0, 0) -124: [20:18:52] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, (0, 0, 1, 0, 0, 0) -124: [20:18:52] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, (0, 0, 1, 0, 0, 0) -124: [20:18:52] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, (0, 0, 1, 0, 0, 0) -124: [20:18:52] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, (0, 10, 0, 0, 0, 0) -124: [20:18:52] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [!#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: [20:18:52] [!#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: [20:18:52] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, (0, 3, 0, 0, 0, 0) -124: [20:18:52] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, (0, 3, 0, 0, 0, 0) -124: [20:18:52] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, (0, 3, 0, 0, 0, 0) -124: [20:18:52] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, (0, 3, 0, 0, 0, 0) -124: [20:18:52] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, (0, 3, 0, 0, 0, 0) -124: [20:18:52] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, (0, 3, 0, 0, 0, 0) -124: [20:18:52] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, (0, 3, 0, 0, 0, 0) -124: [20:18:52] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, (0, 3, 0, 0, 0, 0) -124: ----------- -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, (100, 0, 0, 0, 0, 0) -124: [20:18:52] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, (100, 0, 0, 0, 0, 0) -124: [20:18:52] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, (0, 10, 0, 0, 0, 0) -124: [20:18:52] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, (0, 10, 0, 0, 0, 0) -124: [20:18:52] [!#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: [20:18:52] [!#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: [20:18:52] [!#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: [20:18:52] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, (0, 0, 1, 0, 0, 0) -124: [20:18:52] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, (0, 0, 1, 0, 0, 0) -124: ----------- -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, (0, 0, 4, 0, 0, 0) -124: [20:18:52] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, (100, 0, 0, 0, 0, 0) -124: [20:18:52] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, (0, 10, 0, 0, 0, 0) -124: ----------- -124: ----------- -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, (0, 8, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, (5, 0, 0, 0, 0, 0) -124: [20:18:52] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, (5, 0, 0, 0, 0, 0) -124: [20:18:53] [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: [20:18:53] [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: [20:18:53] [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: [20:18:53] [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: [20:18:53] [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: [20:18:53] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, (0, 0, 2, 0, 0, 0) -124: [20:18:55] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -124: [20:18:55] UFFTYPER: Unrecognized atom type: N_5 (2) -124: [20:18:55] UFFTYPER: Unrecognized atom type: N_5 (3) -124: [20:18:55] UFFTYPER: Unrecognized atom type: N_5 (2) -124: [20:18:55] UFFTYPER: Unrecognized atom type: N_5 (3) -124: [20:18:55] UFFTYPER: Unrecognized charge state for atom: 1 -124: [20:18:55] UFFTYPER: Unrecognized charge state for atom: 1 -124: [20:18:55] UFFTYPER: Unrecognized charge state for atom: 1 -118: [20:18:55] done -118: [20:18:55] ------------------------------------- -118: [20:18:55] Test MMFF multithreading3 -125: .[20:18:56] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:56] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:56] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:56] Molecule does not have explicit Hs. Consider calling AddHs() -125: ..[20:18:56] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -124: [20:18:57] UFFTYPER: Unrecognized charge state for atom: 5 -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: ..[20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -124: [20:18:57] UFFTYPER: Unrecognized charge state for atom: 5 -125: .[20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -124: [20:18:57] UFFTYPER: Unrecognized charge state for atom: 5 -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:57] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -25: Checking against /build/rdkit-202209.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -120: [20:18:58] done -120: [20:18:58] ------------------------------------- -120: [20:18:58] Test UFF multithreading3 -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -124: [20:18:58] UFFTYPER: Unrecognized charge state for atom: 6 -125: [20:18:58] Molecule does not have explicit Hs. Consider calling AddHs() -124: [20:18:59] UFFTYPER: Unrecognized charge state for atom: 6 -124: [20:18:59] UFFTYPER: Unrecognized charge state for atom: 6 -125: [20:18:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:18:59] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:00] Molecule does not have explicit Hs. Consider calling AddHs() -25: All 191 tests passed -25: done -25: ------------------------------------- -25: Unit tests for all MMFF constraint terms. -125: [20:19:00] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:00] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:00] Molecule does not have explicit Hs. Consider calling AddHs() -25: 10.0003 -125: [20:19:01] Molecule does not have explicit Hs. Consider calling AddHs() -25: done -25: ------------------------------------- -25: Unit test for MMFF TorsionConstraint close to 0 degrees. -25: done -25: ------------------------------------- -25: Unit tests for copying MMFF ForceFields. -125: [20:19:01] Molecule does not have explicit Hs. Consider calling AddHs() -25: done -25: ------------------------------------- -25: Unit test for MMFF butane scan. -125: [20:19:01] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:02] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:02] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:02] Molecule does not have explicit Hs. Consider calling AddHs() -118: [20:19:02] done -118: [20:19:02] ------------------------------------- -118: [20:19:02] Testing github 162: Incorrect SMILES after MMFF parameterization . -118: [20:19:02] done -118: [20:19:02] ------------------------------------- -118: [20:19:02] Testing github 224: crash during MMFF parameterization . -118: [20:19:02] done -118/208 Test #118: testMMFFForceFieldHelpers .............. Passed 34.62 sec +120: [07:09:49] Rep: 100 Mol:2 +120: [07:09:49] Rep: 100 Mol:6 +120: [07:09:49] Rep: 100 Mol:10 +120: [07:09:49] Rep: 100 Mol:14 +120: [07:09:49] Rep: 100 Mol:18 +120: [07:09:49] Rep: 100 Mol:22 +120: [07:09:49] Rep: 100 Mol:26 +120: [07:09:49] Rep: 100 Mol:30 +124: [07:09:49] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +124: [07:09:49] UFFTYPER: Unrecognized atom type: N_5 (2) +124: [07:09:49] UFFTYPER: Unrecognized atom type: N_5 (3) +124: [07:09:49] UFFTYPER: Unrecognized atom type: N_5 (2) +124: [07:09:49] UFFTYPER: Unrecognized atom type: N_5 (3) +124: [07:09:49] UFFTYPER: Unrecognized charge state for atom: 1 +124: [07:09:49] UFFTYPER: Unrecognized charge state for atom: 1 +124: [07:09:49] UFFTYPER: Unrecognized charge state for atom: 1 +118: [07:09:50] Rep: 80 Mol:2 +118: [07:09:50] Rep: 80 Mol:6 +118: [07:09:50] Rep: 80 Mol:10 +118: [07:09:50] Rep: 80 Mol:14 +118: [07:09:50] Rep: 80 Mol:18 +118: [07:09:50] Rep: 80 Mol:22 +118: [07:09:50] Rep: 80 Mol:26 +118: [07:09:50] Rep: 80 Mol:30 +124: [07:09:50] UFFTYPER: Unrecognized charge state for atom: 5 +124: [07:09:50] UFFTYPER: Unrecognized charge state for atom: 5 +124: [07:09:50] UFFTYPER: Unrecognized charge state for atom: 5 +124: [07:09:50] UFFTYPER: Unrecognized charge state for atom: 6 +124: [07:09:50] UFFTYPER: Unrecognized charge state for atom: 6 +124: [07:09:50] UFFTYPER: Unrecognized charge state for atom: 6 +118: [07:09:50] done +118: [07:09:50] ------------------------------------- +118: [07:09:50] Test MMFF multithreading2 +125: .[07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: ..[07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: ..[07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:51] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +120: [07:09:52] done +120: [07:09:52] ------------------------------------- +120: [07:09:52] Test UFF multithreading2 +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[07:09:52] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:53] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:53] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:54] Molecule does not have explicit Hs. Consider calling AddHs() +124: [07:09:54] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +123: building molecules +125: [07:09:54] Molecule does not have explicit Hs. Consider calling AddHs() +124: [07:09:54] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +123: generating reference data +124: [07:09:54] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +118: [07:09:54] done +118: [07:09:54] ------------------------------------- +118: [07:09:54] Test MMFF multithreading3 +124: [07:09:54] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: [07:09:55] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +125: [07:09:55] Molecule does not have explicit Hs. Consider calling AddHs() +124: [07:09:55] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +124: =============================================================================== +124: All tests passed (163 assertions in 5 test cases) +124: +118/208 Test #124: distGeomHelpersCatch ................... Passed 6.72 sec test 126 Start 126: testMolAlign 126: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 126: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 126: Test timeout computed to be: 1500 -125: [20:19:02] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:02] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:03] Molecule does not have explicit Hs. Consider calling AddHs() -123: building molecules -125: [20:19:03] Molecule does not have explicit Hs. Consider calling AddHs() -123: generating reference data -125: .[20:19:03] Molecule does not have explicit Hs. Consider calling AddHs() 126: *********************************************************** 126: Testing MolAlign 126: --------------------------------- @@ -24173,16 +24181,52 @@ 126: testIssue241 126: 126: *********************************************************** -119/208 Test #126: testMolAlign ........................... Passed 1.30 sec +119/208 Test #126: testMolAlign ........................... Passed 0.69 sec test 127 Start 127: testO3AAlign 127: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 127: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 127: Test timeout computed to be: 1500 -25: done -125: [20:19:04] Molecule does not have explicit Hs. Consider calling AddHs() -120/208 Test #25: testMMFFForceField ..................... Passed 136.22 sec +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +108: [07:09:56] Warning: molecule is tagged as 3D, but all Z coords are zero +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Test unfolded version of RDKFP +108: [07:09:56] ------------------------------------- +108: [07:09:56] Test bitinfo of RDKFP +108: [07:09:56] ------------------------------------- +108: [07:09:56] Single atoms setting radius 1 bits in Morgan fingerprints +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Github #879: Pattern fingerprint should set bits for single-atom fragments. +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Github #2115: BitInfo not complete for RDKFingerprint +108: [07:09:56] done +108: [07:09:56] ------------------------------------- +108: [07:09:56] Github #3723: Fingerprint crash for mols with Zero order bonds +120/208 Test #108: testFingerprints ....................... Passed 16.16 sec test 128 Start 128: molAlignCatchTest @@ -24192,101 +24236,83 @@ 128: =============================================================================== 128: All tests passed (9 assertions in 1 test case) 128: -121/208 Test #128: molAlignCatchTest ...................... Passed 0.11 sec +121/208 Test #128: molAlignCatchTest ...................... Passed 0.07 sec test 129 Start 129: pyMolAlign 129: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 129: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap 129: Test timeout computed to be: 1500 -120: [20:19:04] done -120: [20:19:04] ------------------------------------- -120: [20:19:04] Testing GitHubIssue62. -120: [20:19:05] beta-lactam 39.6387 -120: [20:19:05] cyclopropanone 174.698 -120: [20:19:05] aziridine 337.986 -120: [20:19:05] aziridinone 115.248 -120: [20:19:05] isobutene 2.48217 -120: [20:19:05] acetone 1.91788 -120: [20:19:05] cyclopentanone 10.1648 -120: [20:19:05] cyclopropene 99.4921 -120: [20:19:05] cyclobutene 41.0156 -120: [20:19:05] cyclopropane 267.236 -120: [20:19:05] gamma-lactam 15.7471 -120: [20:19:05] trans-2,3-diphenylcyclopropan-1-one 203.398 -120: [20:19:05] cis-2,3-diphenylcyclopropan-1-one 206.852 -120: [20:19:05] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -120: [20:19:05] cyclopropylidencyclobutane 218.879 -120: [20:19:05] diphenylmethylidencyclobutane 79.6139 -120: [20:19:05] done -120: [20:19:05] ------------------------------------- -120: [20:19:05] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -120: [20:19:05] done -120: [20:19:05] ------------------------------------- -120: [20:19:05] Test square planar complexes -120: [20:19:05] done -120: [20:19:05] ------------------------------------- -120: [20:19:05] Test octahedral complexes -120: [20:19:05] done -122/208 Test #120: testUFFForceFieldHelpers ............... Passed 35.06 sec +120: [07:09:56] done +120: [07:09:56] ------------------------------------- +120: [07:09:56] Test UFF multithreading3 +118: [07:09:58] done +118: [07:09:58] ------------------------------------- +118: [07:09:58] Testing github 162: Incorrect SMILES after MMFF parameterization . +118: [07:09:58] done +118: [07:09:58] ------------------------------------- +118: [07:09:58] Testing github 224: crash during MMFF parameterization . +118: [07:09:58] done +122/208 Test #118: testMMFFForceFieldHelpers .............. Passed 15.20 sec test 130 Start 130: testFeatures 130: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 130: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 130: Test timeout computed to be: 1500 -130: [20:19:05] ------------------------------------- -130: [20:19:05] AtomType parser testing. -130: [20:19:05] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -130: [20:19:05] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -130: [20:19:05] done -130: [20:19:05] ------------------------------------- -130: [20:19:05] FeatureDefinition parser testing. -130: [20:19:05] done -130: [20:19:05] ------------------------------------- -130: [20:19:05] Test pulling feat defs from a string. -130: [20:19:05] done -130: [20:19:05] ------------------------------------- -130: [20:19:05] FeatureDef functionality testing. -130: [20:19:06] done -130: [20:19:06] ------------------------------------- -130: [20:19:06] FeatureFactory testing. -130: [20:19:06] 1 -130: [20:19:06] 2 -130: [20:19:06] 3 -130: [20:19:06] 4 -130: [20:19:06] 5 -130: [20:19:06] 6 -130: [20:19:06] done -130: [20:19:06] ------------------------------------- -130: [20:19:06] Feature Location testing. -130: [20:19:06] done -130: [20:19:06] ------------------------------------- -130: [20:19:06] Test building a FeatureFactory from a file -130: [20:19:06] done -130: [20:19:06] ------------------------------------- -130: [20:19:06] Testing Issue 224. -130: [20:19:06] done -130: [20:19:06] ------------------------------------- -130: [20:19:06] Testing Issue 225. -130: [20:19:06] done -130: [20:19:06] ------------------------------------- -130: [20:19:06] Test Issue346 -130: [20:19:06] done -130: [20:19:06] ------------------------------------- -130: [20:19:06] Test Issue347 -130: [20:19:06] done -130: [20:19:06] ------------------------------------- -130: [20:19:06] Testing Issue 348. -130: [20:19:06] SMARTS Parse Error: syntax error while parsing: [C[C] -130: [20:19:06] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -130: [20:19:06] ------------------------------------- -130: [20:19:06] Testing Nested AtomType definitions. +125: [07:09:58] Molecule does not have explicit Hs. Consider calling AddHs() +130: [07:09:58] ------------------------------------- +130: [07:09:58] AtomType parser testing. +130: [07:09:58] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +130: [07:09:58] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] FeatureDefinition parser testing. +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Test pulling feat defs from a string. +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] FeatureDef functionality testing. +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] FeatureFactory testing. +130: [07:09:58] 1 +130: [07:09:58] 2 +130: [07:09:58] 3 +130: [07:09:58] 4 +130: [07:09:58] 5 +130: [07:09:58] 6 +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Feature Location testing. +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Test building a FeatureFactory from a file +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Testing Issue 224. +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Testing Issue 225. +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Test Issue346 +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Test Issue347 +130: [07:09:58] done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Testing Issue 348. +130: [07:09:58] SMARTS Parse Error: syntax error while parsing: [C[C] +130: [07:09:58] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +130: [07:09:58] ------------------------------------- +130: [07:09:58] Testing Nested AtomType definitions. 130: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -130: [20:19:06] ------------------------------------- -130: [20:19:06] Testing Github Issue #252: crash when calling getPos() with no conformer. -130: [20:19:06] expect a precondition failure message below -130: [20:19:06] +130: [07:09:58] ------------------------------------- +130: [07:09:58] Testing Github Issue #252: crash when calling getPos() with no conformer. +130: [07:09:58] expect a precondition failure message below +130: [07:09:58] 130: 130: **** 130: Pre-condition Violation @@ -24295,47 +24321,80 @@ 130: Failed Expression: dp_mol->getNumConformers() 130: **** 130: -130: [20:19:06] Done -130: [20:19:06] ------------------------------------- -130: [20:19:06] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -130: [20:19:06] done -123/208 Test #130: testFeatures ........................... Passed 0.11 sec +130: [07:09:58] Done +130: [07:09:58] ------------------------------------- +130: [07:09:58] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +130: [07:09:58] done +123/208 Test #130: testFeatures ........................... Passed 0.08 sec test 131 Start 131: pyChemicalFeatures 131: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 131: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 131: Test timeout computed to be: 1500 -125: [20:19:06] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:07] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:58] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +120: [07:09:59] done +120: [07:09:59] ------------------------------------- +120: [07:09:59] Testing GitHubIssue62. +120: [07:09:59] beta-lactam 39.6387 +120: [07:09:59] cyclopropanone 174.698 +120: [07:09:59] aziridine 337.986 +120: [07:09:59] aziridinone 115.248 131: /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:154: DeprecationWarning: Please use assertTrue instead. 131: self.failUnless(cfac.GetNumFeatureDefs() == 2) +120: [07:09:59] isobutene 2.48217 +120: [07:09:59] acetone 1.91788 +120: [07:09:59] cyclopentanone 10.1648 +120: [07:09:59] cyclopropene 99.4921 131: /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:159: DeprecationWarning: Please use assertFalse instead. 131: self.failIf(m) -131: .[20:19:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[07:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +120: [07:09:59] cyclobutene 41.0156 +120: [07:09:59] cyclopropane 267.236 131: /build/rdkit-202209.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py:48: DeprecationWarning: Please use assertRaises instead. 131: self.failUnlessRaises(IndexError, lambda: cfac.GetMolFeature(mol, 3)) -131: .[20:19:08] Molecule does not have explicit Hs. Consider calling AddHs() -124: [20:19:08] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -125: [20:19:08] Molecule does not have explicit Hs. Consider calling AddHs() -131: ..[20:19:08] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[20:19:08] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[20:19:08] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -131: [20:19:08] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +120: [07:09:59] gamma-lactam 15.7471 +131: .[07:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +120: [07:09:59] trans-2,3-diphenylcyclopropan-1-one 203.398 +120: [07:09:59] cis-2,3-diphenylcyclopropan-1-one 206.852 +131: ..[07:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[07:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[07:09:59] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +131: [07:09:59] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' 131: ... 131: ---------------------------------------------------------------------- -131: Ran 9 tests in 0.568s +131: Ran 9 tests in 0.180s 131: 131: OK -124: [20:19:08] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -124/208 Test #131: pyChemicalFeatures ..................... Passed 3.08 sec +120: [07:09:59] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +120: [07:09:59] cyclopropylidencyclobutane 218.879 +124/208 Test #131: pyChemicalFeatures ..................... Passed 1.59 sec test 132 Start 132: testShapeHelpers 132: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 132: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers 132: Test timeout computed to be: 1500 -124: [20:19:09] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +125: [07:09:59] Molecule does not have explicit Hs. Consider calling AddHs() +120: [07:09:59] diphenylmethylidencyclobutane 79.6139 +120: [07:09:59] done +120: [07:09:59] ------------------------------------- +120: [07:09:59] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +120: [07:09:59] done +120: [07:09:59] ------------------------------------- +120: [07:09:59] Test square planar complexes +120: [07:09:59] done +120: [07:09:59] ------------------------------------- +120: [07:09:59] Test octahedral complexes +120: [07:09:59] done +125/208 Test #120: testUFFForceFieldHelpers ............... Passed 15.64 sec +test 133 + Start 133: pyShapeHelpers + +133: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" +133: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap +133: Test timeout computed to be: 1500 132: *********************************************************** 132: Testing ShapeHelpers 132: --------------------------------- @@ -24348,41 +24407,33 @@ 132: testGithub4364 132: 132: *********************************************************** -125/208 Test #132: testShapeHelpers ....................... Passed 0.17 sec -test 133 - Start 133: pyShapeHelpers - -133: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" -133: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap -133: Test timeout computed to be: 1500 -124: [20:19:09] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -124: [20:19:09] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -125: [20:19:09] Molecule does not have explicit Hs. Consider calling AddHs() -124: [20:19:09] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -124: =============================================================================== -124: All tests passed (163 assertions in 5 test cases) -124: -126/208 Test #124: distGeomHelpersCatch ................... Passed 18.75 sec +126/208 Test #132: testShapeHelpers ....................... Passed 0.09 sec test 134 Start 134: testMolCatalog 134: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 134: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 134: Test timeout computed to be: 1500 -127/208 Test #134: testMolCatalog ......................... Passed 0.12 sec +127/208 Test #134: testMolCatalog ......................... Passed 0.03 sec test 135 Start 135: pyMolCatalog 135: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 135: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 135: Test timeout computed to be: 1500 +125: [07:10:00] Molecule does not have explicit Hs. Consider calling AddHs() +135: . +135: ---------------------------------------------------------------------- +135: Ran 1 test in 0.019s +135: +135: OK 133: . 133: ---------------------------------------------------------------------- -133: Ran 1 test in 0.375s +133: Ran 1 test in 0.127s 133: 133: OK 133: Testing Shape Helpers wrapper -128/208 Test #133: pyShapeHelpers ......................... Passed 2.30 sec +128/208 Test #135: pyMolCatalog ........................... Passed 0.70 sec test 136 Start 136: moldraw2DTest1 @@ -24390,14 +24441,17 @@ 136: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 136: Test timeout computed to be: 1500 136: ----------------- Test 1 -135: . -135: ---------------------------------------------------------------------- -135: Ran 1 test in 0.053s -135: -135: OK +129/208 Test #133: pyShapeHelpers ......................... Passed 0.86 sec +test 137 + Start 137: moldraw2DTestCatch + +137: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +137: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +137: Test timeout computed to be: 1500 136: Done 136: ----------------- Test 2 136: file test2_1.png gave hash 2758573664U not the expected 2505713963U +125: [07:10:00] Molecule does not have explicit Hs. Consider calling AddHs() 136: file test2_2.png gave hash 15206223U not the expected 4058920248U 136: file test2_3.png gave hash 2294574389U not the expected 2179746375U 136: Done @@ -24410,24 +24464,18 @@ 136: file test5_3.png gave hash 3327935566U not the expected 3266389887U 136: Done 136: ----------------- Test 6 (atom labels) -129/208 Test #135: pyMolCatalog ........................... Passed 2.17 sec -test 137 - Start 137: moldraw2DTestCatch - -137: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -137: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -137: Test timeout computed to be: 1500 136: Done 136: ----------------- Test 7 (backgrounds) 136: file test7_1.png gave hash 1318319255U not the expected 3331950391U +137: file testAtomTags_3.svg gave hash 1089318994U not the expected 2131854465U 136: file test7_2.png gave hash 2612306717U not the expected 1686496331U 136: Done 136: ----------------- Test8: PrepareMolDrawing 136: Done 136: ----------------- Test multi-threaded drawing 136: reading molecules -137: file testAtomTags_3.svg gave hash 1089318994U not the expected 2131854465U 136: generating reference drawings +123: validating reference data 136: processing 136: launch :0 136: launch :1 @@ -24437,49 +24485,43 @@ 137: file testGithub3226_2.png gave hash 1518784691U not the expected 2460913971U 137: file testGithub3226_3.png gave hash 1819502787U not the expected 993799198U 137: file testPNGMetadata_1.png gave hash 2101998463U not the expected 2022143293U -125: [20:19:14] Molecule does not have explicit Hs. Consider calling AddHs() 137: file testPNGMetadata_2.png gave hash 3782595494U not the expected 3078435362U -137: [20:19:15] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:15] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:01] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:01] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-1.svg gave hash 1672085979U not the expected 799391905U -137: [20:19:15] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:15] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:01] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:01] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-1.png gave hash 1255474327U not the expected 1551605661U -125: [20:19:15] Molecule does not have explicit Hs. Consider calling AddHs() -137: [20:19:16] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:16] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:02] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:02] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-2.svg gave hash 1532574901U not the expected 2605087576U -137: [20:19:16] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:16] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:02] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:02] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-2.png gave hash 3384312931U not the expected 2979412913U -137: [20:19:16] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:16] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:02] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:02] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-3.svg gave hash 3544722771U not the expected 1015633173U -137: [20:19:16] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:16] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:02] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:02] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-3.png gave hash 330712840U not the expected 1765396301U -137: [20:19:16] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:16] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:02] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:02] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-4.svg gave hash 2804458995U not the expected 830784921U -137: [20:19:16] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:16] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:02] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:02] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-4.png gave hash 2967030530U not the expected 2989933219U -123: validating reference data -125: [20:19:17] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:18] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:20] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:19:22] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[07:10:03] Molecule does not have explicit Hs. Consider calling AddHs() 137: file testHandDrawn-5a.svg gave hash 3564930200U not the expected 2845825621U -137: [20:19:25] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:25] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:05] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:05] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-5b.svg gave hash 1382342714U not the expected 476521352U -137: [20:19:25] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. -137: [20:19:25] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +137: [07:10:05] Font file /build/rdkit-202209.3/Data/Fonts/ComicNeue-Regular.ttf not found. +137: [07:10:05] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. 137: file testHandDrawn-5.png gave hash 3915321151U 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: [20:19:27] unrecognized bond typefile testGithub4238_1.png gave hash 857148181U not the expected 458925131U +137: [07:10:06] unrecognized bond typefile testGithub4238_1.png gave hash 857148181U not the expected 458925131U 137: file testGithub4323_1.png gave hash 446904698U not the expected 3711520691U 127: *********************************************************** 127: Testing O3AAlign @@ -24512,8 +24554,7 @@ 127: 127: generating reference data 137: file testGithub4323_3.png gave hash 218188912U not the expected 2300228708U -137: [20:19:29] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. -125: .[20:19:30] Molecule does not have explicit Hs. Consider calling AddHs() +137: [07:10:07] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 123: processing 123: launch :0 123: launch :1 @@ -24535,13 +24576,13 @@ 137: file acs1996_2.png gave hash 318073570U not the expected 83755168U 137: file acs1996_7.svg gave hash 2718384395U not the expected 763391533U 137: file acs1996_11.svg gave hash 4001805189U not the expected 2121789178U -137: [20:19:36] 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: [07:10:10] 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 1433305237U not the expected 3826056528U 137: =============================================================================== 137: All tests passed (379 assertions in 67 test cases) 137: -130/208 Test #137: moldraw2DTestCatch ..................... Passed 24.30 sec +130/208 Test #137: moldraw2DTestCatch ..................... Passed 10.12 sec test 138 Start 138: moldraw2DRxnTest1 @@ -24550,6 +24591,11 @@ 138: Test timeout computed to be: 1500 138: ----------------- Test 1 138: file rxn_test1_1.png gave hash 1138104440U not the expected 3579100589U +127: processing +127: launch :0 +127: launch :1 +127: launch :2 +127: launch :3 138: file rxn_test1_2.png gave hash 2172746452U not the expected 3996724834U 138: file rxn_test1_3.png gave hash 1768080454U not the expected 4153817948U 138: file rxn_test1_4.png gave hash 3679789417U not the expected 4175225545U @@ -24559,12 +24605,7 @@ 138: file rxn_test1_7.svg gave hash 793051905U not the expected 1748644916U 138: Done 138: ----------------- Test 2: some examples that caused problems in testing -127: processing -127: launch :0 -127: launch :1 -127: launch :2 138: file rxn_test2_1.png gave hash 3728182892U not the expected 2654417911U -127: launch :3 138: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C 138: file rxn_test2_2_1.png gave hash 3926348179U not the expected 997060634U 138: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl @@ -24588,16 +24629,16 @@ 138: file rxn_test4_2.png gave hash 3110572674U not the expected 2842629749U 138: file rxn_test4_2.svg gave hash 2715300209U not the expected 946039978U 138: Done -131/208 Test #138: moldraw2DRxnTest1 ...................... Passed 5.02 sec +131/208 Test #138: moldraw2DRxnTest1 ...................... Passed 1.96 sec test 139 Start 139: pyMolDraw2D 139: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 139: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 139: Test timeout computed to be: 1500 -139: ...[20:19:46] Font file /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -139: [20:19:46] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -139: ..........[20:19:46] +139: ...[07:10:14] Font file /build/rdkit-202209.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +139: [07:10:14] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +139: ..........[07:10:14] 139: 139: **** 139: Pre-condition Violation @@ -24608,10 +24649,10 @@ 139: 139: ................... 139: ---------------------------------------------------------------------- -139: Ran 32 tests in 3.871s +139: Ran 32 tests in 2.204s 139: 139: OK -132/208 Test #139: pyMolDraw2D ............................ Passed 9.39 sec +132/208 Test #139: pyMolDraw2D ............................ Passed 4.00 sec test 140 Start 140: testFMCS @@ -24623,35 +24664,35 @@ 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 0.744 seconds +140: Time elapsed 0.135 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 0.158 seconds +140: Time elapsed 0.020 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 0.223 seconds +140: Time elapsed 0.034 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 1.539 seconds +140: Time elapsed 0.279 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 1.102 seconds +140: Time elapsed 0.242 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 1.622 seconds +140: Time elapsed 0.504 seconds 140: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -140: Time elapsed 1.597 seconds +140: Time elapsed 0.739 seconds 140: 140: testSegFault() 140: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.234 seconds +140: Time elapsed 0.049 seconds 140: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.249 seconds +140: Time elapsed 0.056 seconds 140: MCS MatchFusedRingsStrict: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -140: Time elapsed 0.296 seconds +140: Time elapsed 0.060 seconds 140: 140: testThreshold() 140: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -24659,11 +24700,11 @@ 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 9.108 seconds +140: Time elapsed 2.146 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 7.115 seconds +140: Time elapsed 2.438 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 4.931 seconds +140: Time elapsed 1.787 seconds 140: 140: testAtomCompareIsotopes() 140: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds @@ -24675,39 +24716,39 @@ 140: 140: testAtomCompareAnyAtom() 140: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -140: Time elapsed 0.000 seconds +140: Time elapsed 0.001 seconds 140: 140: testAtomCompareAnyAtom() 140: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -140: Time elapsed 0.009 seconds +140: Time elapsed 0.000 seconds 140: 140: testAtomCompareAnyAtom() 140: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -140: Time elapsed 0.000 seconds +140: Time elapsed 0.001 seconds 140: 140: testJnk1LigandsDistance() 140: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds -140: Time elapsed 0.118 seconds +140: Time elapsed 0.031 seconds 140: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds -140: Time elapsed 0.023 seconds +140: Time elapsed 0.018 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 0.145 seconds +140: Time elapsed 0.026 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 0.962 seconds +140: Time elapsed 0.609 seconds 140: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 140: Time elapsed 0.002 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 0.193 seconds +140: Time elapsed 0.207 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 0.0119 seconds. bond[0]=6 +140: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0151 seconds. bond[0]=6 140: STATISTICS: -140: Total Growing Steps = 1, MCS found on 1 step, for 0.0119 seconds +140: Total Growing Steps = 1, MCS found on 1 step, for 0.0151 seconds 140: Initial Seeds = 1, Mismatched 0 140: Inspected Seeds = 2 140: Rejected by BestSize = 0 @@ -24726,7 +24767,7 @@ 140: HashFoundInCache= 0 140: ExactMatchCalls = 0 140: ExactMatchFound = 0 -140: Time elapsed 0.017 seconds +140: Time elapsed 0.016 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 @@ -24826,26 +24867,26 @@ 140: 140: MCS: [#6]-&!@[#6] 2 atoms, 1 bonds 140: -129: ............[20:20:23] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:25] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:25] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:25] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:25] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:25] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:25] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:26] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:26] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:26] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:26] Molecule does not have explicit Hs. Consider calling AddHs() -140: [20:20:38] The provided InitialSeed is not an MCS and will be ignored +129: ............[07:10:31] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:31] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:31] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:31] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:32] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:32] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:32] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:32] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:32] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:32] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:32] Molecule does not have explicit Hs. Consider calling AddHs() +140: [07:10:33] 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 47.06 seconds -133/208 Test #140: testFMCS ............................... Passed 47.22 sec +140: TOTAL Time elapsed 16.36 seconds +133/208 Test #140: testFMCS ............................... Passed 16.42 sec test 141 Start 141: pyFMCS @@ -24888,17 +24929,12 @@ 136: file test860_3.png gave hash 363974217U not the expected 1675954369U 136: Done 136: ----------------- Test Github #910: ugly coordinates generated for peptide chains -129: ...[20:20:51] Molecule does not have explicit Hs. Consider calling AddHs() 136: Done 136: ----------------- Test Github #932: mistake in SVG for wedged bonds -129: [20:20:51] Molecule does not have explicit Hs. Consider calling AddHs() 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 -129: [20:20:51] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:51] Molecule does not have explicit Hs. Consider calling AddHs() -129: [20:20:51] Molecule does not have explicit Hs. Consider calling AddHs() 136: Done 136: ----------------- Test Deuterium, Tritium 136: Done @@ -24909,12 +24945,6 @@ 136: ----------------- Testing drawing a grid of molecules 136: Done 136: ----------------- Testing drawMolecules -129: ... -129: ---------------------------------------------------------------------- -129: Ran 18 tests in 106.284s -129: -129: OK -129: Testing MolAlign Wrappers 136: Done 136: ----------------- Test JSON Configuration 136: Done @@ -24929,15 +24959,217 @@ 136: ----------------- Testing use of a black & white palette 136: Done 136: ----------------- Testing use of continuous highlighting with drawMolecules -134/208 Test #129: pyMolAlign ............................. Passed 109.20 sec +136: Done +136: ----------------- Test 17 - Testing maximum font size +136: Done +136: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list +136: Done +136: ----------------- Testing use of fixed scales for drawing. +136: Done +136: ----------------- Testing rotation of 2D drawing. +136: Done +136: ----------------- Testing inclusion of molecule metadata +136: Done +136: ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default +136: Done +136: ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions +136: file testGithub2151_1.svg gave hash 2202108456U not the expected 1918752877U +136: file testGithub2151_2.svg gave hash 2417118198U 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: file testGithub2931_1.svg gave hash 550063130U not the expected 142684703U +136: file testGithub2931_3.svg gave hash 4097987949U not the expected 1660359809U +136: Done +136: ----------------- Testing annotation of 2D Drawing. +136: file test20_1.png gave hash 3005935546U not the expected 221585048U +136: file test20_2.png gave hash 1694942689U not the expected 1113799362U +136: file test20_3.png gave hash 652955779U not the expected 1764616972U +136: file test20_4.png gave hash 4274652913U not the expected 781264160U +136: Done +136: ----------------- Test 21 - different font +136: [07:10:35] Font file /build/rdkit-202209.3/Data/Fonts/No_Such_Font_File.ttf not found. +136: [07:10:35] Falling back to original font file /build/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 255418450U not the expected 316930677U +136: file testGithub3305_2.png gave hash 1774822891U not the expected 3520446560U +136: file testGithub3305_3.png gave hash 970935540U not the expected 3960184199U +136: file testGithub3305_4.png gave hash 667377464U not the expected 411486117U +136: [07:10:35] +136: +136: **** +136: Test Assert +136: Expression Failed: +136: Violation occurred on line 4318 in file ./Code/GraphMol/MolDraw2D/test1.cpp +136: Failed Expression: std::regex_search(text, bondMatch, regex) == 1 +136: **** +136: +136: terminate called after throwing an instance of 'Invar::Invariant' +136: what(): Expression Failed: +134/208 Test #136: moldraw2DTest1 .........................Subprocess aborted***Exception: 35.10 sec + ----------------- Test 1 + Done + ----------------- Test 2 +file test2_1.png gave hash 2758573664U not the expected 2505713963U +file test2_2.png gave hash 15206223U not the expected 4058920248U +file test2_3.png gave hash 2294574389U not the expected 2179746375U + Done + ----------------- Test 4 +file test4_1.png gave hash 3244658643U not the expected 1924202631U + Done + ----------------- Test 5 +file test5_1.png gave hash 2220164034U not the expected 2116545562U +file test5_2.png gave hash 502154818U not the expected 1519942634U +file test5_3.png gave hash 3327935566U not the expected 3266389887U + Done + ----------------- Test 6 (atom labels) + Done + ----------------- Test 7 (backgrounds) +file test7_1.png gave hash 1318319255U not the expected 3331950391U +file test7_2.png gave hash 2612306717U not the expected 1686496331U + Done + ----------------- Test8: PrepareMolDrawing + Done + ----------------- Test multi-threaded drawing +reading molecules +generating reference drawings +processing + launch :0 + launch :1 + launch :2 + launch :3 + Done + ----------------- Test Github #781: Rendering single-atom molecules + Done + ----------------- Test 3 +file test3_1.png gave hash 138653240U not the expected 1578780280U +file test3_2.png gave hash 2252903825U not the expected 1100583374U +file test3_3.png gave hash 802419933U not the expected 2405974883U +file test3_3.svg gave hash 3214754201U not the expected 3967096277U +file test3_4.png gave hash 164766785U not the expected 3523404550U +file test3_4.svg gave hash 3380791190U not the expected 1410409071U +file test3_5.png gave hash 667377464U not the expected 411486117U +file test3_5.svg gave hash 1902305684U not the expected 2728740111U +file test3_6.png gave hash 3814422911U not the expected 2817453573U +file test3_7.png gave hash 3884678560U not the expected 285272009U + Done + ----------------- Test Github774: upside-down drawings +file test774_1.png gave hash 1854972040U not the expected 930347428U +file test774_2.png gave hash 2429471214U not the expected 1089219024U + Done + ----------------- Test 9 (molecule legends) +file test9_1.svg gave hash 618149026U not the expected 3204904541U + Done + ----------------- Test Github852: Lines used to wedge bonds are too thick +file test852_1.png gave hash 2417987646U not the expected 4140960740U +file test852_2.png gave hash 245570345U not the expected 4294133823U +---------------- +---------------- +---------------- +---------------- + Done + ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +file test860_1.png gave hash 2024936722U not the expected 1000110983U +file test860_2.png gave hash 223195491U not the expected 4079976606U +file test860_3.png gave hash 363974217U not the expected 1675954369U + Done + ----------------- Test Github #910: ugly coordinates generated for peptide chains + Done + ----------------- Test Github #932: mistake in SVG for wedged bonds + Done + ----------------- Test Github #953: default color should not be cyan + Done + ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly + Done + ----------------- Test Deuterium, Tritium + Done + ----------------- Test crossed bonds + Done + ----------------- Testing drawing a second molecule + Done + ----------------- Testing drawing a grid of molecules + Done + ----------------- Testing drawMolecules + Done + ----------------- Test JSON Configuration + Done + ----------------- Testing github 1090: escape html characters in SVG output + Done + ----------------- Testing github 1035: overflow bug in SVG color generation + Done + ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes + Done + ----------------- Testing github 1322: add custom atom labels + Done + ----------------- Testing use of a black & white palette + Done + ----------------- Testing use of continuous highlighting with drawMolecules + Done + ----------------- Test 17 - Testing maximum font size + Done + ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list + Done + ----------------- Testing use of fixed scales for drawing. + Done + ----------------- Testing rotation of 2D drawing. + Done + ----------------- Testing inclusion of molecule metadata + Done + ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default + Done + ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions +file testGithub2151_1.svg gave hash 2202108456U not the expected 1918752877U +file testGithub2151_2.svg gave hash 2417118198U not the expected 1083134500U + Done + ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn + Done + ----------------- Testing testGithub2931: multi-coloured molecule highlights. +file testGithub2931_1.svg gave hash 550063130U not the expected 142684703U +file testGithub2931_3.svg gave hash 4097987949U not the expected 1660359809U + Done + ----------------- Testing annotation of 2D Drawing. +file test20_1.png gave hash 3005935546U not the expected 221585048U +file test20_2.png gave hash 1694942689U not the expected 1113799362U +file test20_3.png gave hash 652955779U not the expected 1764616972U +file test20_4.png gave hash 4274652913U not the expected 781264160U + Done + ----------------- Test 21 - different font +[07:10:35] Font file /build/rdkit-202209.3/Data/Fonts/No_Such_Font_File.ttf not found. +[07:10:35] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. +Done + ----------------- Test 22 - draw explicit methyls. +Done + ----------------- Testing drawing of legends. + Done + ----------------- Test Github 3305 - change and scale line widths. +file testGithub3305_1.png gave hash 255418450U not the expected 316930677U +file testGithub3305_2.png gave hash 1774822891U not the expected 3520446560U +file testGithub3305_3.png gave hash 970935540U not the expected 3960184199U +file testGithub3305_4.png gave hash 667377464U not the expected 411486117U +[07:10:35] + +**** +Test Assert +Expression Failed: +Violation occurred on line 4318 in file ./Code/GraphMol/MolDraw2D/test1.cpp +Failed Expression: std::regex_search(text, bondMatch, regex) == 1 +**** + +terminate called after throwing an instance of 'Invar::Invariant' + what(): Expression Failed: + test 142 Start 142: FMCStest 142: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 142: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test 142: Test timeout computed to be: 1500 -136: Done -136: ----------------- Test 17 - Testing maximum font size 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 @@ -26694,10 +26926,6 @@ 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 -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. 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 @@ -26907,7 +27135,7 @@ 142: 142: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 142: ERROR: RDKit could not load input file -135/208 Test #142: FMCStest ............................... Passed 0.30 sec +135/208 Test #142: FMCStest ............................... Passed 0.05 sec test 143 Start 143: molHashCatchTest @@ -26917,212 +27145,19 @@ 143: =============================================================================== 143: All tests passed (60 assertions in 5 test cases) 143: -136/208 Test #143: molHashCatchTest ....................... Passed 0.13 sec +136/208 Test #143: molHashCatchTest ....................... Passed 0.16 sec test 144 Start 144: pyMolHash 144: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 144: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 144: 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 2202108456U not the expected 1918752877U -136: file testGithub2151_2.svg gave hash 2417118198U 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: file testGithub2931_1.svg gave hash 550063130U not the expected 142684703U -136: file testGithub2931_3.svg gave hash 4097987949U not the expected 1660359809U -136: Done -136: ----------------- Testing annotation of 2D Drawing. -136: file test20_1.png gave hash 3005935546U not the expected 221585048U -136: file test20_2.png gave hash 1694942689U not the expected 1113799362U -136: file test20_3.png gave hash 652955779U not the expected 1764616972U -136: file test20_4.png gave hash 4274652913U not the expected 781264160U -136: Done -136: ----------------- Test 21 - different font -136: [20:20:56] Font file /build/rdkit-202209.3/Data/Fonts/No_Such_Font_File.ttf not found. -136: [20:20:56] Falling back to original font file /build/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 255418450U not the expected 316930677U -136: file testGithub3305_2.png gave hash 1774822891U not the expected 3520446560U -136: file testGithub3305_3.png gave hash 970935540U not the expected 3960184199U -136: file testGithub3305_4.png gave hash 667377464U not the expected 411486117U -136: [20:20:57] -136: -136: **** -136: Test Assert -136: Expression Failed: -136: Violation occurred on line 4318 in file ./Code/GraphMol/MolDraw2D/test1.cpp -136: Failed Expression: std::regex_search(text, bondMatch, regex) == 1 -136: **** -136: -136: terminate called after throwing an instance of 'Invar::Invariant' -136: what(): Expression Failed: -137/208 Test #136: moldraw2DTest1 .........................Subprocess aborted***Exception: 105.55 sec - ----------------- Test 1 - Done - ----------------- Test 2 -file test2_1.png gave hash 2758573664U not the expected 2505713963U -file test2_2.png gave hash 15206223U not the expected 4058920248U -file test2_3.png gave hash 2294574389U not the expected 2179746375U - Done - ----------------- Test 4 -file test4_1.png gave hash 3244658643U not the expected 1924202631U - Done - ----------------- Test 5 -file test5_1.png gave hash 2220164034U not the expected 2116545562U -file test5_2.png gave hash 502154818U not the expected 1519942634U -file test5_3.png gave hash 3327935566U not the expected 3266389887U - Done - ----------------- Test 6 (atom labels) - Done - ----------------- Test 7 (backgrounds) -file test7_1.png gave hash 1318319255U not the expected 3331950391U -file test7_2.png gave hash 2612306717U not the expected 1686496331U - Done - ----------------- Test8: PrepareMolDrawing - Done - ----------------- Test multi-threaded drawing -reading molecules -generating reference drawings -processing - launch :0 - launch :1 - launch :2 - launch :3 - Done - ----------------- Test Github #781: Rendering single-atom molecules - Done - ----------------- Test 3 -file test3_1.png gave hash 138653240U not the expected 1578780280U -file test3_2.png gave hash 2252903825U not the expected 1100583374U -file test3_3.png gave hash 802419933U not the expected 2405974883U -file test3_3.svg gave hash 3214754201U not the expected 3967096277U -file test3_4.png gave hash 164766785U not the expected 3523404550U -file test3_4.svg gave hash 3380791190U not the expected 1410409071U -file test3_5.png gave hash 667377464U not the expected 411486117U -file test3_5.svg gave hash 1902305684U not the expected 2728740111U -file test3_6.png gave hash 3814422911U not the expected 2817453573U -file test3_7.png gave hash 3884678560U not the expected 285272009U - Done - ----------------- Test Github774: upside-down drawings -file test774_1.png gave hash 1854972040U not the expected 930347428U -file test774_2.png gave hash 2429471214U not the expected 1089219024U - Done - ----------------- Test 9 (molecule legends) -file test9_1.svg gave hash 618149026U not the expected 3204904541U - Done - ----------------- Test Github852: Lines used to wedge bonds are too thick -file test852_1.png gave hash 2417987646U not the expected 4140960740U -file test852_2.png gave hash 245570345U not the expected 4294133823U ----------------- ----------------- ----------------- ----------------- - Done - ----------------- Test Github860: Atom symbols in wrong order if bond comes from right -file test860_1.png gave hash 2024936722U not the expected 1000110983U -file test860_2.png gave hash 223195491U not the expected 4079976606U -file test860_3.png gave hash 363974217U not the expected 1675954369U - Done - ----------------- Test Github #910: ugly coordinates generated for peptide chains - Done - ----------------- Test Github #932: mistake in SVG for wedged bonds - Done - ----------------- Test Github #953: default color should not be cyan - Done - ----------------- Test Github #983: wedged bonds between chiral centers drawn improperly - Done - ----------------- Test Deuterium, Tritium - Done - ----------------- Test crossed bonds - Done - ----------------- Testing drawing a second molecule - Done - ----------------- Testing drawing a grid of molecules - Done - ----------------- Testing drawMolecules - Done - ----------------- Test JSON Configuration - Done - ----------------- Testing github 1090: escape html characters in SVG output - Done - ----------------- Testing github 1035: overflow bug in SVG color generation - Done - ----------------- Testing github 1271: MolDraw2D not drawing anything for molecules aligned with the X or Y axes - Done - ----------------- Testing github 1322: add custom atom labels - Done - ----------------- Testing use of a black & white palette - Done - ----------------- Testing use of continuous highlighting with drawMolecules - Done - ----------------- Test 17 - Testing maximum font size - Done - ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list - Done - ----------------- Testing use of fixed scales for drawing. - Done - ----------------- Testing rotation of 2D drawing. - Done - ----------------- Testing inclusion of molecule metadata - Done - ----------------- Testing Github2063: Drawing racemic bond stereo as crossed bonds should be the default - Done - ----------------- Testing Github2151: MolDraw2D: line width should be controlled by MolDrawOptions -file testGithub2151_1.svg gave hash 2202108456U not the expected 1918752877U -file testGithub2151_2.svg gave hash 2417118198U not the expected 1083134500U - Done - ----------------- Testing testGithub2762: MolDraw2D: HCl and ethane should be drawn - Done - ----------------- Testing testGithub2931: multi-coloured molecule highlights. -file testGithub2931_1.svg gave hash 550063130U not the expected 142684703U -file testGithub2931_3.svg gave hash 4097987949U not the expected 1660359809U - Done - ----------------- Testing annotation of 2D Drawing. -file test20_1.png gave hash 3005935546U not the expected 221585048U -file test20_2.png gave hash 1694942689U not the expected 1113799362U -file test20_3.png gave hash 652955779U not the expected 1764616972U -file test20_4.png gave hash 4274652913U not the expected 781264160U - Done - ----------------- Test 21 - different font -[20:20:56] Font file /build/rdkit-202209.3/Data/Fonts/No_Such_Font_File.ttf not found. -[20:20:56] Falling back to original font file /build/rdkit-202209.3/Data/Fonts/Telex-Regular.ttf. -Done - ----------------- Test 22 - draw explicit methyls. -Done - ----------------- Testing drawing of legends. - Done - ----------------- Test Github 3305 - change and scale line widths. -file testGithub3305_1.png gave hash 255418450U not the expected 316930677U -file testGithub3305_2.png gave hash 1774822891U not the expected 3520446560U -file testGithub3305_3.png gave hash 970935540U not the expected 3960184199U -file testGithub3305_4.png gave hash 667377464U not the expected 411486117U -[20:20:57] - -**** -Test Assert -Expression Failed: -Violation occurred on line 4318 in file ./Code/GraphMol/MolDraw2D/test1.cpp -Failed Expression: std::regex_search(text, bondMatch, regex) == 1 -**** - -terminate called after throwing an instance of 'Invar::Invariant' - what(): Expression Failed: - +144: .. +144: ---------------------------------------------------------------------- +144: Ran 2 tests in 0.050s +144: +144: OK +137/208 Test #144: pyMolHash .............................. Passed 1.18 sec test 145 Start 145: testMMPA @@ -27131,7 +27166,7 @@ 145: Test timeout computed to be: 1500 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -145: Time elapsed 0.016417 seconds +145: Time elapsed 0.015507 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 @@ -27168,16 +27203,11 @@ 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. -144: .. -144: ---------------------------------------------------------------------- -144: Ran 2 tests in 0.128s -144: -144: OK 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: Time elapsed 0.023229 seconds +145: Time elapsed 0.022503 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 @@ -27219,7 +27249,7 @@ 145: ----------------------------------- 145: 145: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -145: Time elapsed 0.007808 seconds +145: Time elapsed 0.018431 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] @@ -27259,7 +27289,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -145: Time elapsed 0.018550 seconds +145: Time elapsed 0.001830 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] @@ -27281,7 +27311,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -145: Time elapsed 0.056864 seconds +145: Time elapsed 0.016375 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 @@ -27324,7 +27354,7 @@ 145: ----------------------------------- 145: 145: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -145: Time elapsed 0.041361 seconds +145: Time elapsed 0.023826 seconds 145: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 145: 1: NOREF. Reference data NOT LISTED in test case. 145: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -27349,13 +27379,6 @@ 145: 11: NOREF. Reference data NOT LISTED in test case. 145: 12: res= NULL,O=C(OCc1ccccc1)[*:1].OC(c1ccccc1)[*:1] 145: 12: NOREF. Reference data NOT LISTED in test case. -138/208 Test #144: pyMolHash .............................. Passed 3.66 sec -test 146 - Start 146: pyMMPA - -146: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" -146: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap -146: Test timeout computed to be: 1500 145: 13: res= c1ccc(C([*:1])[*:2])cc1,O=C(OCc1ccccc1)[*:1].O[*:2] 145: 13: NOREF. Reference data NOT LISTED in test case. 145: 14: res= C([*:1])([*:2])[*:3],O=C(OCc1ccccc1)[*:1].O[*:2].c1ccc([*:3])cc1 @@ -27372,23 +27395,41 @@ 145: --- ALL PASSED --- 145: ----------------------------------- 145: 5 TEST CASES FAILED -139/208 Test #145: testMMPA ............................... Passed 1.11 sec +138/208 Test #145: testMMPA ............................... Passed 0.59 sec +test 146 + Start 146: pyMMPA + +146: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" +146: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap +146: Test timeout computed to be: 1500 +129: ...[07:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +129: [07:10:39] Molecule does not have explicit Hs. Consider calling AddHs() +129: ... +129: ---------------------------------------------------------------------- +129: Ran 18 tests in 41.778s +129: +129: OK +129: Testing MolAlign Wrappers +139/208 Test #129: pyMolAlign ............................. Passed 43.67 sec test 147 Start 147: testCIPLabeler 147: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 147: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler 147: Test timeout computed to be: 1500 -147: [20:20:58] non kekulizable aromatic bond being treated as bond order 1 -147: [20:20:58] non kekulizable aromatic bond being treated as bond order 1 -147: [20:20:58] non kekulizable aromatic bond being treated as bond order 1 -147: [20:20:58] non kekulizable aromatic bond being treated as bond order 1 -147: [20:20:58] non kekulizable aromatic bond being treated as bond order 1 -147: [20:20:58] non kekulizable aromatic bond being treated as bond order 1 +147: [07:10:40] non kekulizable aromatic bond being treated as bond order 1 +147: [07:10:40] non kekulizable aromatic bond being treated as bond order 1 +147: [07:10:40] non kekulizable aromatic bond being treated as bond order 1 +147: [07:10:40] non kekulizable aromatic bond being treated as bond order 1 +147: [07:10:40] non kekulizable aromatic bond being treated as bond order 1 +147: [07:10:40] non kekulizable aromatic bond being treated as bond order 1 147: =============================================================================== 147: All tests passed (5974 assertions in 12 test cases) 147: -140/208 Test #147: testCIPLabeler ......................... Passed 0.23 sec +140/208 Test #147: testCIPLabeler ......................... Passed 0.25 sec test 148 Start 148: pyCIPLabelsWrapTest @@ -27397,10 +27438,10 @@ 148: Test timeout computed to be: 1500 148: ... 148: ---------------------------------------------------------------------- -148: Ran 3 tests in 0.089s +148: Ran 3 tests in 0.019s 148: 148: OK -141/208 Test #148: pyCIPLabelsWrapTest .................... Passed 3.00 sec +141/208 Test #148: pyCIPLabelsWrapTest .................... Passed 1.60 sec test 149 Start 149: pyCIPLabelsValidation @@ -27409,10 +27450,10 @@ 149: Test timeout computed to be: 1500 146: ......... 146: ---------------------------------------------------------------------- -146: Ran 9 tests in 16.301s +146: Ran 9 tests in 4.422s 146: 146: OK -142/208 Test #146: pyMMPA ................................. Passed 19.71 sec +142/208 Test #146: pyMMPA ................................. Passed 5.73 sec test 150 Start 150: deprotectTest @@ -27422,7 +27463,7 @@ 150: =============================================================================== 150: All tests passed (111 assertions in 3 test cases) 150: -143/208 Test #150: deprotectTest .......................... Passed 0.34 sec +143/208 Test #150: deprotectTest .......................... Passed 0.29 sec test 151 Start 151: pyDeprotect @@ -27431,7 +27472,7 @@ 151: Test timeout computed to be: 1500 151: ..... 151: ---------------------------------------------------------------------- -151: Ran 5 tests in 0.603s +151: Ran 5 tests in 0.347s 151: 151: OK 151: Testing tert-butyldimethylsilyl @@ -27484,7 +27525,7 @@ 151: Testing acetamide 151: Testing carbobenzyloxy 151: Testing Acetal/Ketal -144/208 Test #151: pyDeprotect ............................ Passed 4.21 sec +144/208 Test #151: pyDeprotect ............................ Passed 1.33 sec test 152 Start 152: testReducedGraphs @@ -27509,7 +27550,7 @@ 152: 152: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 152: -145/208 Test #152: testReducedGraphs ...................... Passed 0.44 sec +145/208 Test #152: testReducedGraphs ...................... Passed 0.17 sec test 153 Start 153: pyReducedGraphs @@ -27518,488 +27559,488 @@ 153: Test timeout computed to be: 1500 153: ..... 153: ---------------------------------------------------------------------- -153: Ran 5 tests in 0.218s +153: Ran 5 tests in 0.052s 153: 153: OK -146/208 Test #153: pyReducedGraphs ........................ Passed 4.31 sec +146/208 Test #153: pyReducedGraphs ........................ Passed 1.06 sec test 154 Start 154: trajectoryTest 154: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 154: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory 154: Test timeout computed to be: 1500 -147/208 Test #154: trajectoryTest ......................... Passed 4.22 sec +147/208 Test #154: trajectoryTest ......................... Passed 1.15 sec test 155 Start 155: substructLibraryTest 155: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 155: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 155: Test timeout computed to be: 1500 -155: [20:21:31] ------------------------------------- -155: [20:21:31] Test1 -141: ...........................................[20:21:32] The provided InitialSeed is not an MCS and will be ignored -141: [20:21:32] The provided InitialSeed is not an MCS and will be ignored -141: [20:21:32] The provided InitialSeed is not an MCS and will be ignored -141: .[20:21:32] The provided InitialSeed is not an MCS and will be ignored -141: [20:21:32] The provided InitialSeed is not an MCS and will be ignored -141: [20:21:32] The provided InitialSeed is not an MCS and will be ignored -155: [20:21:32] done -155: [20:21:32] ------------------------------------- -155: [20:21:32] Test2 -141: .[20:21:32] The provided InitialSeed is not an MCS and will be ignored -141: [20:21:32] The provided InitialSeed is not an MCS and will be ignored -141: [20:21:32] The provided InitialSeed is not an MCS and will be ignored -141: .[20:21:33] The provided InitialSeed is not an MCS and will be ignored -141: [20:21:33] The provided InitialSeed is not an MCS and will be ignored -141: [20:21:33] The provided InitialSeed is not an MCS and will be ignored +155: [07:10:47] ------------------------------------- +155: [07:10:47] Test1 +141: ...........................................[07:10:47] The provided InitialSeed is not an MCS and will be ignored +141: [07:10:47] The provided InitialSeed is not an MCS and will be ignored +141: [07:10:47] The provided InitialSeed is not an MCS and will be ignored +141: .[07:10:47] The provided InitialSeed is not an MCS and will be ignored +141: [07:10:48] The provided InitialSeed is not an MCS and will be ignored +155: [07:10:48] done +141: [07:10:48] The provided InitialSeed is not an MCS and will be ignored +141: .[07:10:48] The provided InitialSeed is not an MCS and will be ignored +141: [07:10:48] The provided InitialSeed is not an MCS and will be ignored +141: [07:10:48] The provided InitialSeed is not an MCS and will be ignored +155: [07:10:48] ------------------------------------- +155: [07:10:48] Test2 +141: .[07:10:48] The provided InitialSeed is not an MCS and will be ignored +141: [07:10:48] The provided InitialSeed is not an MCS and will be ignored +141: [07:10:48] The provided InitialSeed is not an MCS and will be ignored 141: ................. 141: ---------------------------------------------------------------------- -141: Ran 63 tests in 51.969s +141: Ran 63 tests in 13.832s 141: 141: OK -155: [20:21:34] done -155: [20:21:34] ------------------------------------- -155: [20:21:34] Test3 (stereo options) -155: [20:21:34] Done (stereo options) -155: [20:21:34] ------------------------------------- -155: [20:21:34] Test4 (trusted smiles) -155: [20:21:34] Done (trusted smiles) -155: [20:21:34] ------------------------------------- -155: [20:21:34] Testing C++ docs -155: [20:21:34] Done (C++ doc tests) -155: [20:21:34] ------------------------------------- -155: [20:21:34] Testing C++ ring query: PatternHolder -155: [20:21:34] Done (C++ ring query tests) -155: [20:21:34] ------------------------------------- -155: [20:21:34] Testing C++ ring query: TautomerPatternHolder -155: [20:21:34] Done (C++ ring query tests) -155: [20:21:34] ------------------------------------- -155: [20:21:34] Add Patterns -148/208 Test #141: pyFMCS ................................. Passed 56.86 sec +148/208 Test #141: pyFMCS ................................. Passed 15.17 sec test 156 Start 156: substructLibraryCatchTest 156: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 156: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 156: Test timeout computed to be: 1500 +155: [07:10:49] done +155: [07:10:49] ------------------------------------- +155: [07:10:49] Test3 (stereo options) +155: [07:10:49] Done (stereo options) +155: [07:10:49] ------------------------------------- +155: [07:10:49] Test4 (trusted smiles) 156: =============================================================================== 156: All tests passed (111 assertions in 4 test cases) 156: -149/208 Test #156: substructLibraryCatchTest .............. Passed 1.25 sec +149/208 Test #156: substructLibraryCatchTest .............. Passed 1.00 sec test 157 Start 157: pySubstructLibrary 157: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 157: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap 157: Test timeout computed to be: 1500 -155: [20:21:46] ------------------------------------- -155: [20:21:46] testing PatternHolder -155: [20:21:47] ------------------------------------- -155: [20:21:47] testing TautomerPatternHolder -155: [20:21:49] ------------------------------------- -155: [20:21:49] testSegFaultInHolder -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:49] Done (trusted smiles) +155: [07:10:49] ------------------------------------- +155: [07:10:49] Testing C++ docs +155: [07:10:49] Done (C++ doc tests) +155: [07:10:49] ------------------------------------- +155: [07:10:49] Testing C++ ring query: PatternHolder +155: [07:10:49] Done (C++ ring query tests) +155: [07:10:49] ------------------------------------- +155: [07:10:49] Testing C++ ring query: TautomerPatternHolder +155: [07:10:49] Done (C++ ring query tests) +155: [07:10:49] ------------------------------------- +155: [07:10:49] Add Patterns +155: [07:10:55] ------------------------------------- +155: [07:10:55] testing PatternHolder +155: [07:10:55] ------------------------------------- +155: [07:10:55] testing TautomerPatternHolder +155: [07:10:56] ------------------------------------- +155: [07:10:56] testSegFaultInHolder +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] [07:10:56] [07:10:56] [07:10:56] SMILESSMILES Parse Error: SMILES Parse Error: [07:10:56] SMILES Parse Error: syntax error Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' 155: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] SMILES Parse Error: syntax error while parsing: dsafsdf -155: [20:21:49] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -155: [20:21:49] ------------------------------------- -155: [20:21:49] Results do not depend on numThreads +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES for input: '[07:10:56] SMILES Parse Error: syntax error while parsing: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: +155: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: syntax error[07:10:56] for input: 'dsafsdf[07:10:56] while parsing: SMILES Parse Error: 'SMILESdsafsdfsyntax error +155: Parse Error: +155: while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error[07:10:56] while parsing: SMILES Parse Error: [07:10:56] SMILES Parse Error: syntax errordsafsdfsyntax errorSMILES Parse Error: syntax error while parsing: +155: while parsing: dsafsdf while parsing: dsafsdf +155: [07:10:56] +155: dsafsdf[07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] +155: SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES[07:10:56] [07:10:56] SMILES Parse Error: SMILES Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf'syntax error Parse Error: Failed parsing SMILES 'dsafsdf' for input: ' while parsing: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdfdsafsdf +155: ' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: for input: '[07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] syntax errordsafsdf[07:10:56] SMILES while parsing: 'SMILES Parse Error: dsafsdf +155: Parse Error: Failed parsing SMILES 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[07:10:56] for input: 'dsafsdf[07:10:56] +155: SMILES'SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] SMILES Parse Error: syntax error while parsing: dsafsdf +155: [07:10:56] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +155: [07:10:56] ------------------------------------- +155: [07:10:56] Results do not depend on numThreads 149: VS001: PASSED 149: VS002: PASSED 149: VS003: PASSED @@ -28302,82 +28343,68 @@ 149: VS300: PASSED 149: Check finished: 0 molecules failed. 149: Failed: -150/208 Test #149: pyCIPLabelsValidation .................. Passed 52.98 sec +150/208 Test #149: pyCIPLabelsValidation .................. Passed 17.92 sec test 158 Start 158: testRGroupDecomp 158: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 158: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 158: Test timeout computed to be: 1500 -158: [20:21:59] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -158: [20:21:59] WARNING: not removing hydrogen atom with dummy atom neighbors -127: --------------------------------- -127: test O3A multithreading bug -127: -127: --------------------------------- -127: testCrippenO3A multithreading -127: -127: generating reference data -157: ......[20:22:17] -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: [20:22:17] -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: -127: processing -127: launch :0 -127: launch :1 -127: launch :2 -127: launch :3 -158: iterative -155: [20:22:28] ------------------------------------- -155: [20:22:28] Results do not depend on numThreads (all same) -155: [20:22:29] ------------------------------------- -155: [20:22:29] testTautomerQueries -155: [20:22:29] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -155: [20:22:29] ------------------------------------- -155: [20:22:29] github3881 recursive smarts with rings -151/208 Test #155: substructLibraryTest ................... Passed 57.90 sec +125: .......[07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: .[07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: [07:11:01] Molecule does not have explicit Hs. Consider calling AddHs() +125: . +125: ---------------------------------------------------------------------- +125: Ran 18 tests in 70.140s +125: +125: OK +151/208 Test #125: pyDistGeomHelpers ...................... Passed 71.66 sec test 159 Start 159: testRGroupDecompInternals 159: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 159: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 159: Test timeout computed to be: 1500 -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -159: [20:22:29] WARNING: not removing hydrogen atom with dummy atom neighbors -152/208 Test #159: testRGroupDecompInternals .............. Passed 0.19 sec +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +159: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +152/208 Test #159: testRGroupDecompInternals .............. Passed 0.07 sec test 160 Start 160: rgroupCatchTests @@ -28387,46 +28414,31 @@ 160: =============================================================================== 160: All tests passed (142 assertions in 10 test cases) 160: -153/208 Test #160: rgroupCatchTests ....................... Passed 1.64 sec +153/208 Test #160: rgroupCatchTests ....................... Passed 0.35 sec test 161 Start 161: pyRGroupDecomposition 161: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 161: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 161: Test timeout computed to be: 1500 -125: .......[20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: .[20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: [20:22:35] Molecule does not have explicit Hs. Consider calling AddHs() -125: . -125: ---------------------------------------------------------------------- -125: Ran 18 tests in 219.336s -125: -125: OK -154/208 Test #125: pyDistGeomHelpers ...................... Passed 225.04 sec +158: [07:11:01] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +158: [07:11:01] WARNING: not removing hydrogen atom with dummy atom neighbors +155: [07:11:05] ------------------------------------- +155: [07:11:05] Results do not depend on numThreads (all same) +161: ............... +161: ---------------------------------------------------------------------- +161: Ran 15 tests in 2.852s +161: +161: OK +154/208 Test #161: pyRGroupDecomposition .................. Passed 3.82 sec test 162 Start 162: molInterchangeTest1 162: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 162: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 162: Test timeout computed to be: 1500 +155: [07:11:05] ------------------------------------- +155: [07:11:05] testTautomerQueries 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":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"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":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 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":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.3","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} @@ -28435,70 +28447,69 @@ 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]]}]}]} -155/208 Test #162: molInterchangeTest1 .................... Passed 0.28 sec +155/208 Test #162: molInterchangeTest1 .................... Passed 0.07 sec test 163 Start 163: molInterchangeCatchTest 163: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 163: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 163: Test timeout computed to be: 1500 -163: [20:22:37] unrecognized bond type set to zero while writing -163: [20:22:37] unrecognized bond type set to zero while writing -163: =============================================================================== -163: All tests passed (14 assertions in 1 test case) -163: -156/208 Test #163: molInterchangeCatchTest ................ Passed 0.30 sec +155: [07:11:05] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +155: [07:11:05] ------------------------------------- +155: [07:11:05] github3881 recursive smarts with rings +156/208 Test #155: substructLibraryTest ................... Passed 18.17 sec test 164 Start 164: pyMolInterchange 164: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 164: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 164: Test timeout computed to be: 1500 -158: bulk -164: . -164: ---------------------------------------------------------------------- -164: Ran 1 test in 0.222s -164: -164: OK -157/208 Test #164: pyMolInterchange ....................... Passed 5.31 sec +163: [07:11:05] unrecognized bond type set to zero while writing +163: [07:11:05] unrecognized bond type set to zero while writing +163: =============================================================================== +163: All tests passed (14 assertions in 1 test case) +163: +157/208 Test #163: molInterchangeCatchTest ................ Passed 0.08 sec test 165 Start 165: testSLNParse 165: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 165: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse 165: Test timeout computed to be: 1500 -165: [20:22:43] SLN Parse Error: syntax error while parsing: CH4[I=13] -165: [20:22:43] Failed parsing SLN 'CH4[I=13]' -165: [20:22:43] SLN Parser error: Atom ID 1 appears *after* its ring closure. -165: [20:22:43] SLN Parser error: Ring closure 1 does not have a corresponding opener. -165: [20:22:43] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -165: [20:22:43] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -165: [20:22:43] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -165: [20:22:43] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -165: [20:22:43] SLN Parse Error: syntax error while parsing: CH4 fff -165: [20:22:43] Failed parsing SLN 'CH4 fff' -165: [20:22:43] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -165: [20:22:43] Failed parsing SLN 'C[charge=+1] foo' -165: [20:22:43] Query property 'is' ignored on non-query atom -165: [20:22:43] Query property 'is' ignored on non-query atom -158/208 Test #165: testSLNParse ........................... Passed 0.39 sec +165: [07:11:05] SLN Parse Error: syntax error while parsing: CH4[I=13] +165: [07:11:05] Failed parsing SLN 'CH4[I=13]' +165: [07:11:05] SLN Parser error: Atom ID 1 appears *after* its ring closure. +165: [07:11:05] SLN Parser error: Ring closure 1 does not have a corresponding opener. +165: [07:11:05] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +165: [07:11:05] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +165: [07:11:05] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +165: [07:11:05] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +165: [07:11:05] SLN Parse Error: syntax error while parsing: CH4 fff +165: [07:11:05] Failed parsing SLN 'CH4 fff' +165: [07:11:05] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +165: [07:11:05] Failed parsing SLN 'C[charge=+1] foo' +165: [07:11:05] Query property 'is' ignored on non-query atom +165: [07:11:05] Query property 'is' ignored on non-query atom +158/208 Test #165: testSLNParse ........................... Passed 0.08 sec test 166 Start 166: pySLNParse 166: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" 166: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 166: Test timeout computed to be: 1500 -157: ............ -157: ---------------------------------------------------------------------- -157: Ran 18 tests in 63.294s -157: -157: OK -157: Testing atom rings -157: testing bond rings -157: searching atom rings -157: searching bond rings -157: done -159/208 Test #157: pySubstructLibrary ..................... Passed 68.41 sec +127: --------------------------------- +127: test O3A multithreading bug +127: +127: --------------------------------- +127: testCrippenO3A multithreading +127: +127: generating reference data +164: . +164: ---------------------------------------------------------------------- +164: Ran 1 test in 0.021s +164: +164: OK +159/208 Test #164: pyMolInterchange ....................... Passed 0.74 sec test 167 Start 167: pyGraphMolWrap @@ -28509,57 +28520,57 @@ 166: self.failUnless(m1) 166: .. 166: ---------------------------------------------------------------------- -166: Ran 2 tests in 0.145s +166: Ran 2 tests in 0.019s 166: 166: OK -167: ..............[20:22:47] SMARTS Parse Error: syntax error while parsing: fiib -167: [20:22:47] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -160/208 Test #166: pySLNParse ............................. Passed 4.38 sec +160/208 Test #166: pySLNParse ............................. Passed 0.93 sec test 168 Start 168: pyTestConformerWrap 168: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Wrap/testConformer.py" 168: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 168: Test timeout computed to be: 1500 -167: ....[20:22:48] ERROR: Problems encountered parsing data fields -167: [20:22:48] ERROR: moving to the beginning of the next molecule -167: [20:22:48] ERROR: Problems encountered parsing data fields -167: [20:22:48] ERROR: moving to the beginning of the next molecule -167: [20:22:48] Spurious data before the first property will be ignored -167: [20:22:48] Property will be truncated after the first blank line -167: [20:22:48] Property will be truncated after the first blank line -167: [20:22:48] Property will be truncated after the first blank line -167: [20:22:48] ERROR: Problems encountered parsing data fields -167: [20:22:48] ERROR: moving to the beginning of the next molecule -167: [20:22:48] ERROR: Problems encountered parsing data fields -167: [20:22:48] ERROR: moving to the beginning of the next molecule -167: [20:22:48] Spurious data before the first property will be ignored -167: [20:22:48] Property will be truncated after the first blank line -167: [20:22:48] Property will be truncated after the first blank line -167: [20:22:48] Property will be truncated after the first blank line -167: [20:22:48] ERROR: Problems encountered parsing data fields -167: [20:22:48] ERROR: moving to the beginning of the next molecule -167: [20:22:48] Property will be truncated after the first blank line -167: [20:22:48] ERROR: Problems encountered parsing data fields -167: [20:22:48] ERROR: moving to the beginning of the next molecule -167: [20:22:48] Property will be truncated after the first blank line -167: .[20:22:48] SMILES Parse Error: syntax error while parsing: fail -167: [20:22:48] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -167: [20:22:48] ERROR: Smiles parse error on line 2 -167: [20:22:48] ERROR: Cannot create molecule from : 'fail' +167: ..............[07:11:07] SMARTS Parse Error: syntax error while parsing: fiib +167: [07:11:07] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +167: ....[07:11:07] ERROR: Problems encountered parsing data fields +167: [07:11:07] ERROR: moving to the beginning of the next molecule +167: [07:11:07] ERROR: Problems encountered parsing data fields +167: [07:11:07] ERROR: moving to the beginning of the next molecule +167: [07:11:07] Spurious data before the first property will be ignored +167: [07:11:07] Property will be truncated after the first blank line +167: [07:11:07] Property will be truncated after the first blank line +167: [07:11:07] Property will be truncated after the first blank line +167: [07:11:07] ERROR: Problems encountered parsing data fields +167: [07:11:07] ERROR: moving to the beginning of the next molecule +167: [07:11:07] ERROR: Problems encountered parsing data fields +167: [07:11:07] ERROR: moving to the beginning of the next molecule +167: [07:11:07] Spurious data before the first property will be ignored +167: [07:11:07] Property will be truncated after the first blank line +167: [07:11:07] Property will be truncated after the first blank line +167: [07:11:07] Property will be truncated after the first blank line +167: [07:11:07] ERROR: Problems encountered parsing data fields +167: [07:11:07] ERROR: moving to the beginning of the next molecule +167: [07:11:07] Property will be truncated after the first blank line +167: [07:11:07] ERROR: Problems encountered parsing data fields +167: [07:11:07] ERROR: moving to the beginning of the next molecule +167: [07:11:07] Property will be truncated after the first blank line +167: .[07:11:07] SMILES Parse Error: syntax error while parsing: fail +167: [07:11:07] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +167: [07:11:07] ERROR: Smiles parse error on line 2 +167: [07:11:07] ERROR: Cannot create molecule from : 'fail' 167: >>> This may result in an infinite loop. It should finish almost instantly 167: <<< OK, it finished. -167: ............[20:22:48] Explicit valence for atom # 1 C, 5, is greater than permitted +168: ...... +168: ---------------------------------------------------------------------- +168: Ran 6 tests in 0.029s +168: +168: OK +167: ............[07:11:07] Explicit valence for atom # 1 C, 5, is greater than permitted 167: ........../build/rdkit-202209.3/Code/GraphMol/Wrap/rough_test.py:2161: DeprecationWarning: Please use assertEqual instead. 167: self.assertEquals(ri.NumRings(), 2) -161: ............... -161: ---------------------------------------------------------------------- -161: Ran 15 tests in 14.541s -161: -161: OK -167: ..[20:22:49] non-ring atom 0 marked aromatic -167: [20:22:49] non-ring atom 0 marked aromatic -167: [20:22:49] +167: ..[07:11:07] non-ring atom 0 marked aromatic +167: [07:11:07] non-ring atom 0 marked aromatic +167: [07:11:07] 167: 167: **** 167: Range Error @@ -28568,9 +28579,16 @@ 167: Failed Expression: 12 < 6 167: **** 167: -167: [20:22:49] non-ring atom 0 marked aromatic -167: [20:22:49] non-ring atom 0 marked aromatic -167: [20:22:49] +167: [07:11:07] non-ring atom 0 marked aromatic +161/208 Test #168: pyTestConformerWrap .................... Passed 0.64 sec +test 169 + Start 169: pyTestTrajectory + +169: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Wrap/testTrajectory.py" +169: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +169: Test timeout computed to be: 1500 +167: [07:11:07] non-ring atom 0 marked aromatic +167: [07:11:07] 167: 167: **** 167: Range Error @@ -28579,31 +28597,27 @@ 167: Failed Expression: 12 < 6 167: **** 167: -167: ...............[20:22:49] 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: [20:22:49] 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. -161/208 Test #161: pyRGroupDecomposition .................. Passed 18.45 sec -test 169 - Start 169: pyTestTrajectory - -169: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Wrap/testTrajectory.py" -169: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -169: Test timeout computed to be: 1500 -167: ..............[20:22:50] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -167: [20:22:50] Explicit valence for atom # 1 C, 5, is greater than permitted -168: ...... -168: ---------------------------------------------------------------------- -168: Ran 6 tests in 0.118s -168: -168: OK -158: bulk, no symmetry -162/208 Test #168: pyTestConformerWrap .................... Passed 4.10 sec +167: ...............[07:11:07] 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: [07:11:07] 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. +127: processing +127: launch :0 +127: launch :1 +127: launch :2 +127: launch :3 +167: ..............[07:11:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +167: [07:11:07] Explicit valence for atom # 1 C, 5, is greater than permitted +29: [07:11:08] Finished +29: [07:11:08] ------------------------------------- +29: [07:11:08] Test github1843: RWMol.clear() should not destroy ring pointer. +29: [07:11:08] Finished +162/208 Test #29: graphmolTest1 .......................... Passed 111.40 sec test 170 Start 170: pyTestSGroups 170: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Wrap/testSGroups.py" 170: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 170: Test timeout computed to be: 1500 -169: [20:22:52] +169: [07:11:08] 169: 169: **** 169: Pre-condition Violation @@ -28612,7 +28626,7 @@ 169: Failed Expression: from < static_cast(size()) 169: **** 169: -169: .[20:22:52] +169: .[07:11:08] 169: 169: **** 169: Pre-condition Violation @@ -28621,7 +28635,22 @@ 169: Failed Expression: from < static_cast(size()) 169: **** 169: -169: .[20:22:54] +170: ............. +170: ---------------------------------------------------------------------- +170: Ran 13 tests in 0.093s +170: +170: OK +170: Testing SubstanceGroups wrapper +163/208 Test #170: pyTestSGroups .......................... Passed 1.03 sec +test 171 + Start 171: pyTestThreads + +171: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Wrap/testThreads.py" +171: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +171: Test timeout computed to be: 1500 +158: iterative +171: [07:11:10] Warning: molecule is tagged as 3D, but all Z coords are zero +169: .[07:11:10] 169: 169: **** 169: Range Error @@ -28630,7 +28659,7 @@ 169: Failed Expression: 0 < 0 169: **** 169: -169: .[20:22:54] +169: .[07:11:10] 169: 169: **** 169: Pre-condition Violation @@ -28639,7 +28668,7 @@ 169: Failed Expression: traj.dimension() == 3 169: **** 169: -169: ..[20:22:54] +169: ..[07:11:10] 169: 169: **** 169: Pre-condition Violation @@ -28648,7 +28677,7 @@ 169: Failed Expression: traj.dimension() == 3 169: **** 169: -169: .[20:22:54] +169: .[07:11:10] 169: 169: **** 169: Pre-condition Violation @@ -28657,7 +28686,7 @@ 169: Failed Expression: d_pos 169: **** 169: -169: [20:22:54] +169: [07:11:10] 169: 169: **** 169: Pre-condition Violation @@ -28666,7 +28695,7 @@ 169: Failed Expression: d_trajectory 169: **** 169: -169: .[20:22:54] +169: .[07:11:10] 169: 169: **** 169: Range Error @@ -28675,7 +28704,7 @@ 169: Failed Expression: 5 < 5 169: **** 169: -169: [20:22:54] +169: [07:11:10] 169: 169: **** 169: Range Error @@ -28684,7 +28713,7 @@ 169: Failed Expression: 10 < 10 169: **** 169: -169: .[20:22:54] +169: .[07:11:10] 169: 169: **** 169: Range Error @@ -28693,7 +28722,7 @@ 169: Failed Expression: 5 < 5 169: **** 169: -169: [20:22:54] +169: [07:11:10] 169: 169: **** 169: Pre-condition Violation @@ -28702,7 +28731,7 @@ 169: Failed Expression: d_trajectory->dimension() == 2 169: **** 169: -169: [20:22:54] +169: [07:11:10] 169: 169: **** 169: Pre-condition Violation @@ -28713,24 +28742,29 @@ 169: 169: . 169: ---------------------------------------------------------------------- -169: Ran 9 tests in 2.676s +169: Ran 9 tests in 1.592s 169: 169: OK 169: Testing Trajectory wrapper -170: ............. -170: ---------------------------------------------------------------------- -170: Ran 13 tests in 0.267s -170: -170: OK -170: Testing SubstanceGroups wrapper -163/208 Test #169: pyTestTrajectory ....................... Passed 5.85 sec -test 171 - Start 171: pyTestThreads - -171: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Wrap/testThreads.py" -171: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -171: Test timeout computed to be: 1500 -164/208 Test #170: pyTestSGroups .......................... Passed 3.54 sec +157: ......[07:11:10] +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: [07:11:10] +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: +164/208 Test #169: pyTestTrajectory ....................... Passed 3.31 sec test 172 Start 172: pyTestMultithreadedMolSupplier @@ -28739,35 +28773,33 @@ 172: Test timeout computed to be: 1500 172: .s. 172: ---------------------------------------------------------------------- -172: Ran 3 tests in 0.446s +172: Ran 3 tests in 0.323s 172: 172: OK (skipped=1) 172: Testing Smiles and SD MultithreadedMolSupplier -171: [20:22:58] Warning: molecule is tagged as 3D, but all Z coords are zero -165/208 Test #172: pyTestMultithreadedMolSupplier ......... Passed 3.58 sec +165/208 Test #172: pyTestMultithreadedMolSupplier ......... Passed 1.64 sec test 173 Start 173: pyTestPropertyLists 173: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Wrap/testPropertyLists.py" 173: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 173: Test timeout computed to be: 1500 -158: [20:22:59] Relabelling existing label -173: [20:23:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [20:23:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [20:23:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -173: .[20:23:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [20:23:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [20:23:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -173: ..[20:23:02] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -173: [20:23:02] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -173: [20:23:02] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +158: bulk +173: [07:11:12] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [07:11:12] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [07:11:12] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: .[07:11:12] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [07:11:12] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [07:11:12] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +173: ..[07:11:12] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +173: [07:11:12] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +173: [07:11:12] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. 173: . 173: ---------------------------------------------------------------------- -173: Ran 4 tests in 0.072s +173: Ran 4 tests in 0.022s 173: 173: OK -158: Best mapping -166/208 Test #173: pyTestPropertyLists .................... Passed 3.79 sec +166/208 Test #173: pyTestPropertyLists .................... Passed 0.65 sec test 174 Start 174: pyCDXMLTest @@ -28776,115 +28808,133 @@ 174: Test timeout computed to be: 1500 174: . 174: ---------------------------------------------------------------------- -174: Ran 1 test in 0.065s +174: Ran 1 test in 0.034s 174: 174: OK -167/208 Test #171: pyTestThreads .......................... Passed 10.94 sec +167/208 Test #174: pyCDXMLTest ............................ Passed 0.63 sec test 175 Start 175: molStandardizeTest 175: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 175: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 175: Test timeout computed to be: 1500 -168/208 Test #174: pyCDXMLTest ............................ Passed 3.53 sec +158: bulk, no symmetry +167: ...........................[07:11:15] unable to set wavy bonds for double bonds: 3 +167: .........[07:11:15] +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: +158: [07:11:16] Relabelling existing label +168/208 Test #175: molStandardizeTest ..................... Passed 2.96 sec test 176 Start 176: molNormalizeTest 176: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 176: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 176: Test timeout computed to be: 1500 -176: [20:23:06] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -176: [20:23:07] Initializing Normalizer -176: [20:23:07] Running Normalizer -176: [20:23:07] Rule applied: BrokenazidetoN=N+=N- -176: [20:23:07] Initializing Normalizer -176: [20:23:07] Running Normalizer -176: [20:23:07] Initializing Normalizer -176: [20:23:07] Running Normalizer -169/208 Test #176: molNormalizeTest ....................... Passed 1.46 sec +176: [07:11:16] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +176: [07:11:16] Initializing Normalizer +176: [07:11:16] Running Normalizer +176: [07:11:16] Rule applied: BrokenazidetoN=N+=N- +176: [07:11:16] Initializing Normalizer +176: [07:11:16] Running Normalizer +176: [07:11:16] Initializing Normalizer +176: [07:11:16] Running Normalizer +169/208 Test #176: molNormalizeTest ....................... Passed 0.25 sec test 177 Start 177: molValidateTest 177: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 177: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 177: Test timeout computed to be: 1500 -170/208 Test #177: molValidateTest ........................ Passed 0.62 sec +170/208 Test #177: molValidateTest ........................ Passed 0.13 sec test 178 Start 178: molChargeTest 178: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 178: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 178: Test timeout computed to be: 1500 -171/208 Test #178: molChargeTest .......................... Passed 1.18 sec +171/208 Test #178: molChargeTest .......................... Passed 0.17 sec test 179 Start 179: molTautomerTest 179: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 179: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 179: Test timeout computed to be: 1500 -172/208 Test #175: molStandardizeTest ..................... Passed 9.72 sec +158: Best mapping +167: ...................[07:11:17] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:17] Explicit valence for atom # 6 F, 2, is greater than permitted +167: [07:11:17] Can't kekulize mol. Unkekulized atoms: 3 4 5 +167: .[07:11:17] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [07:11:17] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [07:11:17] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [07:11:17] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [07:11:17] Warning: molecule is tagged as 3D, but all Z coords are zero +167: [07:11:17] Warning: molecule is tagged as 3D, but all Z coords are zero +179: [07:11:18] Tautomer enumeration stopped at 292 tautomers: max transforms reached +172/208 Test #171: pyTestThreads .......................... Passed 9.94 sec test 180 Start 180: molStandardizeSmallTest 180: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 180: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 180: Test timeout computed to be: 1500 -179: [20:23:16] Tautomer enumeration stopped at 292 tautomers: max transforms reached -173/208 Test #180: molStandardizeSmallTest ................ Passed 0.67 sec +173/208 Test #180: molStandardizeSmallTest ................ Passed 0.16 sec test 181 Start 181: molFragmentTest 181: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 181: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 181: Test timeout computed to be: 1500 -181: [20:23:17] SMARTS Parse Error: syntax error while parsing: [Cl -181: [20:23:17] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -174/208 Test #181: molFragmentTest ........................ Passed 0.78 sec +179: [07:11:19] Tautomer enumeration stopped at 292 tautomers: max transforms reached +181: [07:11:19] SMARTS Parse Error: syntax error while parsing: [Cl +181: [07:11:19] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +174/208 Test #181: molFragmentTest ........................ Passed 0.22 sec test 182 Start 182: molStandardizeCatchTest 182: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 182: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 182: Test timeout computed to be: 1500 +179: [07:11:19] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 182: * - * - * - * m1 182: * - * - * - * m2 182: * - * - * - * m1 182: * - * - * - * m2 -182: [20:23:20] Can't kekulize mol. Unkekulized atoms: 3 7 -182: [20:23:20] Can't kekulize mol. Unkekulized atoms: 3 8 -182: [20:23:20] Can't kekulize mol. Unkekulized atoms: 2 3 4 +179: [07:11:20] Tautomer enumeration stopped at 23 tautomers: canceled +179: Enumeration was canceled due to timeout (50 ms) +182: [07:11:20] Can't kekulize mol. Unkekulized atoms: 3 7 +182: [07:11:20] Can't kekulize mol. Unkekulized atoms: 3 8 +182: [07:11:20] Can't kekulize mol. Unkekulized atoms: 2 3 4 182: =============================================================================== 182: All tests passed (240 assertions in 36 test cases) 182: -175/208 Test #182: molStandardizeCatchTest ................ Passed 3.08 sec +175/208 Test #182: molStandardizeCatchTest ................ Passed 1.03 sec test 183 Start 183: pyMolStandardize 183: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 183: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap 183: Test timeout computed to be: 1500 -179: [20:23:21] Tautomer enumeration stopped at 292 tautomers: max transforms reached -179: [20:23:22] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -179: [20:23:24] Tautomer enumeration stopped at 5 tautomers: canceled -179: Enumeration was canceled due to timeout (50 ms) -167: ...........................[20:23:26] unable to set wavy bonds for double bonds: 3 -167: .........[20:23:27] -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: -183: .....[20:23:30] Tautomer enumeration stopped at 292 tautomers: max transforms reached -183: [20:23:31] Tautomer enumeration stopped at 50 tautomers: max tautomers reached 179: 375 179: Enumeration has completed -183: .[20:23:34] Tautomer enumeration stopped at 4 tautomers: canceled -183: Enumeration was canceled due to timeout (50 ms) -179: [20:23:34] Tautomer enumeration stopped at 14 tautomers: canceled -176/208 Test #158: testRGroupDecomp ....................... Passed 101.28 sec +179: [07:11:23] Tautomer enumeration stopped at 23 tautomers: canceled +157: ............ +157: ---------------------------------------------------------------------- +157: Ran 18 tests in 33.943s +157: +157: OK +157: Testing atom rings +157: testing bond rings +157: searching atom rings +157: searching bond rings +157: done +176/208 Test #157: pySubstructLibrary ..................... Passed 34.85 sec test 184 Start 184: testScaffoldNetwork @@ -28898,91 +28948,78 @@ 179: CN=c1cccc[nH]1 179: CNc1ccccn1 179: res: CNc1ccccn1 -167: ...................[20:23:43] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:23:43] Explicit valence for atom # 6 F, 2, is greater than permitted -167: [20:23:43] Can't kekulize mol. Unkekulized atoms: 3 4 5 -167: .[20:23:43] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [20:23:43] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [20:23:43] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [20:23:43] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [20:23:43] Warning: molecule is tagged as 3D, but all Z coords are zero -167: [20:23:43] Warning: molecule is tagged as 3D, but all Z coords are zero -183: [20:23:44] Tautomer enumeration stopped at 324 tautomers: canceled -183: Enumeration was canceled due to timeout (10 s) -183: [20:23:44] Tautomer enumeration stopped at 5 tautomers: canceled -177/208 Test #179: molTautomerTest ........................ Passed 35.88 sec +183: .....[07:11:24] Tautomer enumeration stopped at 292 tautomers: max transforms reached +177/208 Test #179: molTautomerTest ........................ Passed 7.82 sec test 185 Start 185: pyScaffoldNetwork 185: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 185: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 185: Test timeout computed to be: 1500 -183: ...............[20:23:46] Explicit valence for atom # 1 O, 3, is greater than permitted -183: . -183: ---------------------------------------------------------------------- -183: Ran 22 tests in 21.694s -183: -183: OK -183: done -178/208 Test #183: pyMolStandardize ....................... Passed 26.62 sec +183: [07:11:24] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +185: ....... +185: ---------------------------------------------------------------------- +185: Ran 7 tests in 0.110s +185: +185: OK +183: .[07:11:25] Tautomer enumeration stopped at 21 tautomers: canceled +183: Enumeration was canceled due to timeout (50 ms) +178/208 Test #185: pyScaffoldNetwork ...................... Passed 0.66 sec test 186 Start 186: pyScaffoldNetworkPickling 186: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 186: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 186: Test timeout computed to be: 1500 -185: ....... -185: ---------------------------------------------------------------------- -185: Ran 7 tests in 0.650s -185: -185: OK 186: . 186: ---------------------------------------------------------------------- -186: Ran 1 test in 0.223s +186: Ran 1 test in 0.048s 186: 186: OK -179/208 Test #185: pyScaffoldNetwork ...................... Passed 5.96 sec +179/208 Test #186: pyScaffoldNetworkPickling .............. Passed 1.20 sec test 187 Start 187: testMolEnumerator 187: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 187: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 187: Test timeout computed to be: 1500 -180/208 Test #186: pyScaffoldNetworkPickling .............. Passed 4.33 sec +187: [07:11:26] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +187: =============================================================================== +187: All tests passed (247 assertions in 12 test cases) +187: +180/208 Test #187: testMolEnumerator ...................... Passed 0.24 sec test 188 Start 188: pyMolEnumerator 188: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 188: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 188: Test timeout computed to be: 1500 -187: [20:23:52] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -187: =============================================================================== -187: All tests passed (247 assertions in 12 test cases) -187: -181/208 Test #187: testMolEnumerator ...................... Passed 0.76 sec +181/208 Test #158: testRGroupDecomp ....................... Passed 27.13 sec test 189 Start 189: testAbbreviations 189: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 189: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 189: Test timeout computed to be: 1500 -189: [20:23:52] SMARTS Parse Error: syntax error while parsing: *fail -189: [20:23:52] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -189: [20:23:52] no suitable SubstanceGroups found +189: [07:11:27] SMARTS Parse Error: syntax error while parsing: *fail +189: [07:11:27] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +189: [07:11:27] no suitable SubstanceGroups found 189: =============================================================================== 189: All tests passed (195 assertions in 12 test cases) 189: -182/208 Test #189: testAbbreviations ...................... Passed 0.20 sec +182/208 Test #189: testAbbreviations ...................... Passed 0.15 sec test 190 Start 190: pyAbbreviations 190: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 190: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 190: Test timeout computed to be: 1500 -184: =============================================================================== -184: All tests passed (266 assertions in 18 test cases) -184: -183/208 Test #184: testScaffoldNetwork .................... Passed 17.11 sec +188: ... +188: ---------------------------------------------------------------------- +188: Ran 3 tests in 0.061s +188: +188: OK +183/208 Test #188: pyMolEnumerator ........................ Passed 1.23 sec test 191 Start 191: testQuery @@ -29006,7 +29043,7 @@ 191: XOr 191: pointer and copy foo 191: Set2 -184/208 Test #191: testQuery .............................. Passed 0.05 sec +184/208 Test #191: testQuery .............................. Passed 0.02 sec test 192 Start 192: testMatCalc @@ -29058,63 +29095,69 @@ 192: 9.49496e+07 192: 2.25618e+08 192: 1.30219e+08 -185/208 Test #192: testMatCalc ............................ Passed 0.04 sec +185/208 Test #192: testMatCalc ............................ Passed 0.01 sec test 193 Start 193: pyMatCalc 193: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 193: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 193: Test timeout computed to be: 1500 -188: ... -188: ---------------------------------------------------------------------- -188: Ran 3 tests in 0.252s -188: -188: OK -186/208 Test #188: pyMolEnumerator ........................ Passed 4.36 sec +190: ....... +190: ---------------------------------------------------------------------- +190: Ran 7 tests in 0.076s +190: +190: OK +186/208 Test #190: pyAbbreviations ........................ Passed 1.26 sec test 194 Start 194: testSimDivPickers 194: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 194: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers 194: Test timeout computed to be: 1500 -194: [20:23:56] ------------------------------------- -194: [20:23:56] Testing github issue 1421: MaxMinPicker picking non-existent element. -194: [20:23:56] Done -194: [20:23:56] ------------------------------------- -194: [20:23:56] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -194: [20:23:56] Done -187/208 Test #194: testSimDivPickers ...................... Passed 0.05 sec +194: [07:11:28] ------------------------------------- +194: [07:11:28] Testing github issue 1421: MaxMinPicker picking non-existent element. +194: [07:11:28] Done +194: [07:11:28] ------------------------------------- +194: [07:11:28] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +194: [07:11:28] Done +187/208 Test #194: testSimDivPickers ...................... Passed 0.02 sec test 195 Start 195: pickersTestsCatch 195: Test command: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 195: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers 195: Test timeout computed to be: 1500 -190: ....... -190: ---------------------------------------------------------------------- -190: Ran 7 tests in 0.301s -190: -190: OK 195: =============================================================================== 195: All tests passed (21267 assertions in 1 test case) 195: -188/208 Test #195: pickersTestsCatch ...................... Passed 0.80 sec +184: =============================================================================== +184: All tests passed (266 assertions in 18 test cases) +184: +188/208 Test #195: pickersTestsCatch ...................... Passed 0.29 sec test 196 Start 196: pySimDivPickers 196: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/SimDivPickers/Wrap/testPickers.py" 196: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 196: Test timeout computed to be: 1500 -189/208 Test #190: pyAbbreviations ........................ Passed 4.63 sec +189/208 Test #184: testScaffoldNetwork .................... Passed 4.71 sec test 197 Start 197: pyRanker 197: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/ML/InfoTheory/Wrap/testRanker.py" 197: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 197: Test timeout computed to be: 1500 +183: Enumeration has completed +183: [07:11:29] Tautomer enumeration stopped at 19 tautomers: canceled +196: [07:11:29] the useCache argument is deprecated and ignored +193: ..... +193: ---------------------------------------------------------------------- +193: Ran 5 tests in 1.046s +193: +193: OK 197: ../build/rdkit-202209.3/Code/ML/InfoTheory/Wrap/testRanker.py:124: DeprecationWarning: Please use assertRaisesRegex instead. 197: with self.assertRaisesRegexp(Exception, ""): -197: [20:24:00] +197: [07:11:30] 197: 197: **** 197: Invariant Violation @@ -29125,11 +29168,10 @@ 197: 197: ... 197: ---------------------------------------------------------------------- -197: Ran 5 tests in 0.251s +197: Ran 5 tests in 0.135s 197: 197: OK -196: [20:24:00] the useCache argument is deprecated and ignored -190/208 Test #197: pyRanker ............................... Passed 3.67 sec +190/208 Test #193: pyMatCalc .............................. Passed 1.98 sec test 198 Start 198: testChemicalFeatures @@ -29139,75 +29181,50 @@ 198: ----------------------------------------- 198: Test1 198: Done -191/208 Test #198: testChemicalFeatures ................... Passed 0.03 sec +191/208 Test #198: testChemicalFeatures ................... Passed 0.01 sec test 199 Start 199: pyFeatures 199: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Code/ChemicalFeatures/Wrap/testFeatures.py" 199: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap 199: Test timeout computed to be: 1500 -196: ...[20:24:02] the useCache argument is deprecated and ignored -196: [20:24:02] the useCache argument is deprecated and ignored -196: .[20:24:02] the useCache argument is deprecated and ignored -193: ..... -193: ---------------------------------------------------------------------- -193: Ran 5 tests in 6.929s -193: -193: OK -192/208 Test #193: pyMatCalc .............................. Passed 11.14 sec +196: ...[07:11:30] the useCache argument is deprecated and ignored +196: [07:11:30] the useCache argument is deprecated and ignored +192/208 Test #197: pyRanker ............................... Passed 1.55 sec test 200 Start 200: pythonTestDbCLI 200: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/Projects/test_list.py" "--testDir" "/build/rdkit-202209.3/Projects" 200: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/Projects 200: Test timeout computed to be: 1500 +196: .[07:11:30] the useCache argument is deprecated and ignored 199: .. 199: ---------------------------------------------------------------------- -199: Ran 2 tests in 0.014s +199: Ran 2 tests in 0.004s 199: 199: OK 199: Testing ChemicalFeatures Wrapper code: -193/208 Test #199: pyFeatures ............................. Passed 4.85 sec +193/208 Test #199: pyFeatures ............................. Passed 0.85 sec test 201 Start 201: pythonTestDirRoot 201: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit" 201: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit 201: Test timeout computed to be: 1500 -29: [20:24:06] Finished -29: [20:24:06] ------------------------------------- -29: [20:24:06] Test github1843: RWMol.clear() should not destroy ring pointer. -29: [20:24:06] Finished -194/208 Test #29: graphmolTest1 .......................... Passed 436.52 sec +183: ...............[07:11:31] Explicit valence for atom # 1 O, 3, is greater than permitted +183: . +183: ---------------------------------------------------------------------- +183: Ran 22 tests in 8.855s +183: +183: OK +183: done +194/208 Test #183: pyMolStandardize ....................... Passed 10.80 sec test 202 Start 202: pythonTestDirML 202: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/ML/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/ML" 202: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit 202: Test timeout computed to be: 1500 -201: ......................... -201: ---------------------------------------------------------------------- -201: Ran 25 tests in 2.149s -201: -201: OK -195/208 Test #201: pythonTestDirRoot ...................... Passed 4.08 sec -test 203 - Start 203: pythonTestDirDataStructs - -203: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/DataStructs" -203: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit -203: Test timeout computed to be: 1500 -127: --------------------------------- -127: test getO3AForProbeConfs -127: -127: *********************************************************** -196/208 Test #127: testO3AAlign ........................... Passed 307.76 sec -test 204 - Start 204: pythonTestDirDbase - -204: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/Dbase/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/Dbase" -204: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit -204: Test timeout computed to be: 1500 202: EEEEEEE 202: ====================================================================== 202: ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -29329,53 +29346,128 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 7 tests in 1.098s +202: Ran 7 tests in 0.110s 202: 202: FAILED (errors=7) -196: ....... -196: ---------------------------------------------------------------------- -196: Ran 11 tests in 13.801s -196: -196: OK -203: ....... -203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.269s -203: -203: OK -204: .. -204: ---------------------------------------------------------------------- -204: Ran 2 tests in 0.081s -204: -204: OK -197/208 Test #196: pySimDivPickers ........................ Passed 17.62 sec -test 205 - Start 205: pythonTestDirSimDivFilters +201: ......................... +201: ---------------------------------------------------------------------- +201: Ran 25 tests in 1.276s +201: +201: OK +195/208 Test #201: pythonTestDirRoot ...................... Passed 1.96 sec +test 203 + Start 203: pythonTestDirDataStructs -205: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/SimDivFilters" -205: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit -205: Test timeout computed to be: 1500 -200: [20:24:14] INFO: Reading molecules and constructing molecular database. -200: -200: [20:24:14] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [20:24:14] INFO: Processing 10 molecules -200: -200: [20:24:15] INFO: Generating fingerprints and descriptors: -200: -204: ........... -204: ---------------------------------------------------------------------- -204: Ran 11 tests in 0.168s -204: -204: OK -200: [20:24:15] INFO: Finished. -200: -203: ............../build/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 0.034s -203: -203: OK +203: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/DataStructs" +203: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit +203: Test timeout computed to be: 1500 +167: ...............[07:11:33] +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: [07:11:33] +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: [07:11:33] +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: [07:11:33] +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: [07:11:33] +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: .....[07:11:33] +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: ......[07:11:33] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +167: [07:11:33] ERROR: Smiles parse error on line 0 +167: [07:11:33] ERROR: Cannot create molecule from : 'c1ccccc' +167: [07:11:33] SMILES Parse Error: extra open parentheses for input: 'C(C' +167: [07:11:33] ERROR: Smiles parse error on line 3 +167: [07:11:33] ERROR: Cannot create molecule from : 'C(C' +167: [07:11:33] Explicit valence for atom # 1 C, 5, is greater than permitted +167: [07:11:33] ERROR: Could not sanitize molecule on line 6 +167: [07:11:33] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +167: [07:11:33] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +167: [07:11:33] ERROR: Smiles parse error on line 0 +167: [07:11:33] ERROR: Cannot create molecule from : 'c1ccccc' +167: [07:11:33] SMILES Parse Error: extra open parentheses for input: 'C(C' +167: [07:11:33] ERROR: Smiles parse error on line 3 +167: [07:11:33] ERROR: Cannot create molecule from : 'C(C' +167: [07:11:33] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +167: [07:11:33] ERROR: Smiles parse error on line 6 +167: [07:11:33] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +167: [07:11:33] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:33] ERROR: Could not sanitize molecule ending on line 21 +167: [07:11:33] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:33] ERROR: EOF hit while reading atoms +167: [07:11:33] ERROR: moving to the beginning of the next molecule +167: [07:11:33] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:33] ERROR: Could not sanitize molecule ending on line 21 +167: [07:11:33] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:33] ERROR: EOF hit while reading atoms +167: [07:11:33] ERROR: moving to the beginning of the next molecule +167: ....[07:11:33] +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: ......[07:11:33] +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: ..[07:11:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +167: .................[07:11:33] SMILES Parse Error: unclosed ring for input: 'C1CC' +167: ......[07:11:33] WARNING: not removing hydrogen atom without neighbors +167: [07:11:33] WARNING: not removing hydrogen atom with dummy atom neighbors +167: [07:11:33] WARNING: not removing hydrogen atom with wedged bond +167: [07:11:33] WARNING: not removing hydrogen atom without neighbors +167: [07:11:33] WARNING: not removing hydrogen atom with dummy atom neighbors 202: EEEEEEEEEEEE 202: ====================================================================== 202: ERROR: test10_filtering (__main__.TestCase.test10_filtering) @@ -29582,50 +29674,58 @@ 202: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 202: 202: ---------------------------------------------------------------------- -202: Ran 12 tests in 0.857s +202: Ran 12 tests in 0.335s 202: 202: FAILED (errors=12) -204: . -204: ---------------------------------------------------------------------- -204: Ran 1 test in 0.019s -204: -204: OK -204: ../build/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 0.067s -204: -204: OK -198/208 Test #205: pythonTestDirSimDivFilters ............. Passed 3.56 sec -test 206 - Start 206: pythonTestDirVLib - -206: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/VLib/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/VLib" -206: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit -206: Test timeout computed to be: 1500 -203: ..... +167: .....[07:11:34] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: .[07:11:34] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:34] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:34] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:34] Explicit valence for atom # 1 F, 2, is greater than permitted +167: [07:11:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: [07:11:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: [07:11:34] Can't kekulize mol. Unkekulized atoms: 0 1 2 +167: ..........[07:11:34] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +167: [07:11:34] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +167: .[07:11:34] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +167: [07:11:34] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +167: ..[07:11:34] SMILES Parse Error: syntax error while parsing: error +167: [07:11:34] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +167: [07:11:34] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +167: [07:11:34] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +167: [07:11:34] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +203: ....... 203: ---------------------------------------------------------------------- -203: Ran 5 tests in 0.086s +203: Ran 7 tests in 0.102s 203: 203: OK -204: ...... -204: ---------------------------------------------------------------------- -204: Ran 6 tests in 0.053s -204: -204: OK -199/208 Test #204: pythonTestDirDbase ..................... Passed 7.64 sec -test 207 - Start 207: pythonTestSping +167: ...........[07:11:34] SMILES Parse Error: syntax error while parsing: garbage_0 +167: [07:11:34] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +167: [07:11:34] SMILES Parse Error: syntax error while parsing: garbage_2 +167: [07:11:34] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +167: [07:11:34] SMILES Parse Error: syntax error while parsing: garbage_4 +167: [07:11:34] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +167: ......... +167: ---------------------------------------------------------------------- +167: Ran 228 tests in 27.503s +167: +167: OK +167: 1 +167: supplier: +167: supplier: +167: supplier: +127: --------------------------------- +127: test getO3AForProbeConfs +127: +127: *********************************************************** +196/208 Test #127: testO3AAlign ........................... Passed 98.63 sec +test 204 + Start 204: pythonTestDirDbase -207: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/sping" -207: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit -207: Test timeout computed to be: 1500 -206: ............. -206: ---------------------------------------------------------------------- -206: Ran 13 tests in 0.196s -206: -206: OK +204: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/Dbase/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/Dbase" +204: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit +204: Test timeout computed to be: 1500 202: Traceback (most recent call last): 202: File "/build/rdkit-202209.3/rdkit/ML/UnitTestAnalyzeComposite.py", line 44, in test1_Issue163 202: res = sorted(AnalyzeComposite.ProcessIt([c1, c2], verbose=-1)) @@ -29649,207 +29749,142 @@ 202: AssertionError: 0 is not true 202: 202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.542s +202: Ran 1 test in 0.073s 202: 202: FAILED (failures=1) -167: ...............[20:24:20] -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: [20:24:20] -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: [20:24:20] -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: [20:24:20] -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: [20:24:20] -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: .....[20:24:20] -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: ......[20:24:21] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -167: [20:24:21] ERROR: Smiles parse error on line 0 -167: [20:24:21] ERROR: Cannot create molecule from : 'c1ccccc' -167: [20:24:21] SMILES Parse Error: extra open parentheses for input: 'C(C' -167: [20:24:21] ERROR: Smiles parse error on line 3 -167: [20:24:21] ERROR: Cannot create molecule from : 'C(C' -167: [20:24:21] Explicit valence for atom # 1 C, 5, is greater than permitted -167: [20:24:21] ERROR: Could not sanitize molecule on line 6 -167: [20:24:21] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -167: [20:24:21] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -167: [20:24:21] ERROR: Smiles parse error on line 0 -167: [20:24:21] ERROR: Cannot create molecule from : 'c1ccccc' -167: [20:24:21] SMILES Parse Error: extra open parentheses for input: 'C(C' -167: [20:24:21] ERROR: Smiles parse error on line 3 -167: [20:24:21] ERROR: Cannot create molecule from : 'C(C' -167: [20:24:21] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -167: [20:24:21] ERROR: Smiles parse error on line 6 -167: [20:24:21] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -167: [20:24:21] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:21] ERROR: Could not sanitize molecule ending on line 21 -167: [20:24:21] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:21] ERROR: EOF hit while reading atoms -167: [20:24:21] ERROR: moving to the beginning of the next molecule -167: [20:24:21] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:21] ERROR: Could not sanitize molecule ending on line 21 -167: [20:24:21] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:21] ERROR: EOF hit while reading atoms -167: [20:24:21] ERROR: moving to the beginning of the next molecule -167: ....[20:24:21] -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: ......[20:24:21] -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: ..[20:24:21] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -167: .................[20:24:21] SMILES Parse Error: unclosed ring for input: 'C1CC' -167: ......[20:24:21] WARNING: not removing hydrogen atom without neighbors -167: [20:24:21] WARNING: not removing hydrogen atom with dummy atom neighbors -167: [20:24:21] WARNING: not removing hydrogen atom with wedged bond -167: [20:24:21] WARNING: not removing hydrogen atom without neighbors -167: [20:24:21] WARNING: not removing hydrogen atom with dummy atom neighbors +197/208 Test #167: pyGraphMolWrap ......................... Passed 28.43 sec +test 205 + Start 205: pythonTestDirSimDivFilters + +205: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/SimDivFilters" +205: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit +205: Test timeout computed to be: 1500 +196: ....... +196: ---------------------------------------------------------------------- +196: Ran 11 tests in 5.101s +196: +196: OK +198/208 Test #196: pySimDivPickers ........................ Passed 6.10 sec +test 206 + Start 206: pythonTestDirVLib + +206: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/VLib/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/VLib" +206: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit +206: Test timeout computed to be: 1500 +200: [07:11:35] INFO: Reading molecules and constructing molecular database. +200: +200: [07:11:35] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [07:11:35] INFO: Processing 10 molecules +200: +200: [07:11:35] INFO: Generating fingerprints and descriptors: +200: +203: ............../build/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 0.019s +203: +203: OK +204: .. +204: ---------------------------------------------------------------------- +204: Ran 2 tests in 0.024s +204: +204: OK +200: [07:11:35] INFO: Finished. +200: +202: ... +202: ---------------------------------------------------------------------- +202: Ran 3 tests in 0.004s +202: +202: OK +204: ........... +204: ---------------------------------------------------------------------- +204: Ran 11 tests in 0.108s +204: +204: OK +206: ............. +206: ---------------------------------------------------------------------- +206: Ran 13 tests in 0.085s +206: +206: OK +199/208 Test #205: pythonTestDirSimDivFilters ............. Passed 1.49 sec +test 207 + Start 207: pythonTestSping + +207: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/sping" +207: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit +207: Test timeout computed to be: 1500 +203: ..... +203: ---------------------------------------------------------------------- +203: Ran 5 tests in 0.033s +203: +203: OK +202: ........ +202: ---------------------------------------------------------------------- +202: Ran 8 tests in 0.002s +202: +202: OK +204: . +204: ---------------------------------------------------------------------- +204: Ran 1 test in 0.007s +204: +204: OK +204: ../build/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 0.030s +204: +204: OK +204: ...... +204: ---------------------------------------------------------------------- +204: Ran 6 tests in 0.022s +204: +204: OK 203: ....... 203: ---------------------------------------------------------------------- -203: Ran 7 tests in 0.019s +203: Ran 7 tests in 0.003s 203: 203: OK -200/208 Test #203: pythonTestDirDataStructs ............... Passed 13.15 sec +200/208 Test #204: pythonTestDirDbase ..................... Passed 2.73 sec test 208 Start 208: pythonTestDirChem 208: Test command: /usr/bin/python3.11 "/build/rdkit-202209.3/rdkit/Chem/test_list.py" "--testDir" "/build/rdkit-202209.3/rdkit/Chem" "--buildType" "None" 208: Working Directory: /build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit/Chem 208: Test timeout computed to be: 1500 -167: .....[20:24:23] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: .[20:24:23] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:23] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:23] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:23] Explicit valence for atom # 1 F, 2, is greater than permitted -167: [20:24:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: [20:24:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 -167: [20:24:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 -202: ... -202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.012s -202: -202: OK -167: ..........[20:24:23] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -167: [20:24:23] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -167: .[20:24:23] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -167: [20:24:23] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -167: ..[20:24:23] SMILES Parse Error: syntax error while parsing: error -167: [20:24:23] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -167: [20:24:23] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -167: [20:24:23] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -167: [20:24:23] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -167: ...........[20:24:24] SMILES Parse Error: syntax error while parsing: garbage_0 -167: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -167: [20:24:24] SMILES Parse Error: syntax error while parsing: garbage_2 -167: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -167: [20:24:24] SMILES Parse Error: syntax error while parsing: garbage_4 -167: [20:24:24] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -200: [20:24:24] INFO: Reading molecules and constructing molecular database. -200: -200: [20:24:24] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [20:24:24] INFO: Processing 163 molecules -200: -167: ......... -167: ---------------------------------------------------------------------- -167: Ran 228 tests in 96.490s -167: -167: OK -167: 1 -167: supplier: -167: supplier: -167: supplier: +201/208 Test #203: pythonTestDirDataStructs ............... Passed 4.52 sec 206: ........... 206: ---------------------------------------------------------------------- -206: Ran 11 tests in 0.502s +206: Ran 11 tests in 0.089s 206: 206: OK -201/208 Test #167: pyGraphMolWrap ......................... Passed 100.29 sec -200: [20:24:25] INFO: done 100 +200: [07:11:37] INFO: Reading molecules and constructing molecular database. 200: -202/208 Test #206: pythonTestDirVLib ...................... Passed 7.61 sec -200: [20:24:25] INFO: Generating fingerprints and descriptors: +200: [07:11:37] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [07:11:37] INFO: Processing 163 molecules +200: +202/208 Test #206: pythonTestDirVLib ...................... Passed 2.87 sec +200: [07:11:38] INFO: done 100 200: -202: ........ -202: ---------------------------------------------------------------------- -202: Ran 8 tests in 0.002s -202: -202: OK 207: .. 207: ---------------------------------------------------------------------- -207: Ran 2 tests in 2.174s +207: Ran 2 tests in 0.395s 207: 207: OK -203/208 Test #207: pythonTestSping ........................ Passed 8.59 sec -208: ....... -208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.667s -208: -208: OK +200: [07:11:38] INFO: Generating fingerprints and descriptors: +200: +203/208 Test #207: pythonTestSping ........................ Passed 2.17 sec 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 3.036s +202: Ran 4 tests in 0.972s 202: 202: OK -208: ...... +208: ....... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 0.470s +208: Ran 7 tests in 0.185s 208: 208: OK 202: E.EEE @@ -29910,21 +29945,12 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.045s +202: Ran 5 tests in 0.015s 202: 202: FAILED (errors=4) -208: ....[20:24:35] -208: -208: **** -208: Pre-condition Violation -208: valence not defined for atoms not associated with molecules -208: Violation occurred on line 422 in file ./Code/GraphMol/Atom.cpp -208: Failed Expression: dp_mol -208: **** -208: -208: . +208: ...... 208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.088s +208: Ran 6 tests in 0.082s 208: 208: OK 202: .......E. @@ -29939,29 +29965,43 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 9 tests in 0.059s +202: Ran 9 tests in 0.009s 202: 202: FAILED (errors=1) -208: .... +208: ....[07:11:40] +208: +208: **** +208: Pre-condition Violation +208: valence not defined for atoms not associated with molecules +208: Violation occurred on line 422 in file ./Code/GraphMol/Atom.cpp +208: Failed Expression: dp_mol +208: **** +208: +208: . 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.088s +208: Ran 5 tests in 0.019s 208: 208: OK 202: ............ 202: ---------------------------------------------------------------------- -202: Ran 12 tests in 0.022s +202: Ran 12 tests in 0.007s 202: 202: OK -208: .. +208: .... 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.090s +208: Ran 4 tests in 0.023s 208: 208: OK 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.161s +202: Ran 5 tests in 0.043s 202: 202: OK +208: .. +208: ---------------------------------------------------------------------- +208: Ran 2 tests in 0.019s +208: +208: OK 202: ********************************************************************** 202: File "/build/rdkit-202209.3/rdkit/ML/Data/SplitData.py", line 208, in __main__.SplitDbData 202: Failed example: @@ -30157,12 +30197,17 @@ 202: ***Test Failed*** 14 failures. 208: ...................... 208: ---------------------------------------------------------------------- -208: Ran 22 tests in 0.264s +208: Ran 22 tests in 0.063s 208: 208: OK 202: !!! TEST FAILURE: python UnitTestFilter.py {} 202: !!! TEST FAILURE: python UnitTestMLData.py {} 202: !!! TEST FAILURE: python SplitData.py {} +202: . +202: ---------------------------------------------------------------------- +202: Ran 1 test in 0.001s +202: +202: OK 208: .....s..........E......ss 208: ====================================================================== 208: ERROR: testIpc (__main__.TestCase.testIpc) @@ -30185,59 +30230,49 @@ 208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 208: 208: ---------------------------------------------------------------------- -208: Ran 25 tests in 0.745s +208: Ran 25 tests in 0.279s 208: 208: FAILED (errors=1, skipped=3) -202: . -202: ---------------------------------------------------------------------- -202: Ran 1 test in 0.001s -202: -202: OK 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.012s +202: Ran 6 tests in 0.004s 202: 202: OK 208: ..s 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 1.011s +208: Ran 3 tests in 0.315s 208: 208: OK (skipped=1) -208: ................................... -208: ---------------------------------------------------------------------- -208: Ran 35 tests in 1.235s -208: -208: OK -200: [20:24:53] INFO: Finished. -200: -208: .... -208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.121s -208: -208: OK 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 5.201s +202: Ran 4 tests in 1.296s 202: 202: OK 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 0.146s +202: Ran 6 tests in 0.054s 202: 202: OK -208: . +208: ................................... +208: ---------------------------------------------------------------------- +208: Ran 35 tests in 1.097s +208: +208: OK +200: [07:11:46] INFO: Finished. +200: +208: .... 208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.099s +208: Ran 4 tests in 0.087s 208: 208: OK 202: .. 202: ---------------------------------------------------------------------- -202: Ran 2 tests in 0.910s +202: Ran 2 tests in 0.315s 202: 202: OK -208: ....... +208: . 208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.247s +208: Ran 1 test in 0.022s 208: 208: OK 202: ........E. @@ -30256,25 +30291,30 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 10 tests in 0.077s +202: Ran 10 tests in 0.025s 202: 202: FAILED (errors=1) -208: ... -208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.250s -208: -208: OK 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.495s +202: Ran 5 tests in 0.149s 202: 202: OK +208: ....... +208: ---------------------------------------------------------------------- +208: Ran 7 tests in 0.155s +208: +208: OK 202: !!! TEST FAILURE: python UnitTestQuantTree.py {} 202: .. 202: ---------------------------------------------------------------------- -202: Ran 2 tests in 0.017s +202: Ran 2 tests in 0.010s 202: 202: OK +208: ... +208: ---------------------------------------------------------------------- +208: Ran 3 tests in 0.096s +208: +208: OK 202: ....Traceback (most recent call last): 202: File "/build/rdkit-202209.3/obj-aarch64-linux-gnu/rdkit/ML/Descriptors/MoleculeDescriptors.py", line 88, in CalcDescriptors 202: res[i] = fn(mol) @@ -30301,20 +30341,15 @@ 202: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 202: 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 0.074s +202: Ran 5 tests in 0.056s 202: 202: FAILED (errors=1) 202: ... 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.057s +202: Ran 3 tests in 0.034s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestMolDescriptors.py {} -208: .ss.ss....... -208: ---------------------------------------------------------------------- -208: Ran 13 tests in 7.608s -208: -208: OK (skipped=4) 202: EEE 202: ====================================================================== 202: ERROR: test0CorrMat (__main__.TestCase.test0CorrMat) @@ -30341,17 +30376,22 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 3 tests in 0.004s +202: Ran 3 tests in 0.003s 202: 202: FAILED (errors=3) 202: !!! TEST FAILURE: python UnitTestCorrMatGen.py {} -208: [20:25:14] Molecule does not have explicit Hs. Consider calling AddHs() -208: .[20:25:14] Molecule does not have explicit Hs. Consider calling AddHs() +208: .ss.ss....... +208: ---------------------------------------------------------------------- +208: Ran 13 tests in 2.407s +208: +208: OK (skipped=4) +208: [07:11:52] Molecule does not have explicit Hs. Consider calling AddHs() 202: ...... 202: ---------------------------------------------------------------------- -202: Ran 6 tests in 1.962s +202: Ran 6 tests in 0.769s 202: 202: OK +208: .[07:11:52] Molecule does not have explicit Hs. Consider calling AddHs() 202: ...EE.. 202: ====================================================================== 202: ERROR: testPerm1 (__main__.TestCase.testPerm1) @@ -30370,43 +30410,23 @@ 202: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 202: 202: ---------------------------------------------------------------------- -202: Ran 7 tests in 0.508s +202: Ran 7 tests in 0.172s 202: 202: FAILED (errors=2) 202: !!! TEST FAILURE: python UnitTestPackage.py {} 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.052s +202: Ran 4 tests in 0.021s 202: 202: OK -200: .........[20:25:51] INFO: Reading molecules and constructing molecular database. -200: -200: [20:25:51] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [20:25:51] INFO: Processing 10 molecules -200: -200: [20:25:52] INFO: Generating fingerprints and descriptors: -200: -200: [20:25:52] INFO: Finished. -200: 202: ..... 202: ---------------------------------------------------------------------- -202: Ran 5 tests in 29.825s +202: Ran 5 tests in 6.279s 202: 202: OK -200: [20:25:57] INFO: Reading molecules and constructing molecular database. -200: -200: [20:25:57] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -200: -200: [20:25:57] INFO: Processing 10 molecules -200: -200: [20:25:57] INFO: Generating fingerprints and descriptors: -200: -200: [20:25:57] INFO: Finished. -200: 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.034s +202: Ran 4 tests in 0.004s 202: 202: OK 202: .... @@ -30416,7 +30436,7 @@ 202: OK 202: .... 202: ---------------------------------------------------------------------- -202: Ran 4 tests in 0.050s +202: Ran 4 tests in 0.009s 202: 202: OK 202: !!! TEST FAILURE: python UnitTestBuildComposite.py {} @@ -30427,7 +30447,7 @@ 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'} -204/208 Test #202: pythonTestDirML ........................***Failed 115.17 sec +204/208 Test #202: pythonTestDirML ........................***Failed 31.83 sec EEEEEEE ====================================================================== ERROR: test1_basics (__main__.TestCase.test1_basics) @@ -30549,7 +30569,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 7 tests in 1.098s +Ran 7 tests in 0.110s FAILED (errors=7) EEEEEEEEEEEE @@ -30758,7 +30778,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 12 tests in 0.857s +Ran 12 tests in 0.335s FAILED (errors=12) Traceback (most recent call last): @@ -30784,12 +30804,12 @@ AssertionError: 0 is not true ---------------------------------------------------------------------- -Ran 1 test in 0.542s +Ran 1 test in 0.073s FAILED (failures=1) ... ---------------------------------------------------------------------- -Ran 3 tests in 0.012s +Ran 3 tests in 0.004s OK ........ @@ -30799,7 +30819,7 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 3.036s +Ran 4 tests in 0.972s OK E.EEE @@ -30860,7 +30880,7 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 5 tests in 0.045s +Ran 5 tests in 0.015s FAILED (errors=4) .......E. @@ -30875,17 +30895,17 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 9 tests in 0.059s +Ran 9 tests in 0.009s FAILED (errors=1) ............ ---------------------------------------------------------------------- -Ran 12 tests in 0.022s +Ran 12 tests in 0.007s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.161s +Ran 5 tests in 0.043s OK ********************************************************************** @@ -31091,22 +31111,22 @@ OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.012s +Ran 6 tests in 0.004s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 5.201s +Ran 4 tests in 1.296s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.146s +Ran 6 tests in 0.054s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.910s +Ran 2 tests in 0.315s OK ........E. @@ -31125,18 +31145,18 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 10 tests in 0.077s +Ran 10 tests in 0.025s FAILED (errors=1) ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.495s +Ran 5 tests in 0.149s OK !!! TEST FAILURE: python UnitTestQuantTree.py {} .. ---------------------------------------------------------------------- -Ran 2 tests in 0.017s +Ran 2 tests in 0.010s OK ....Traceback (most recent call last): @@ -31165,12 +31185,12 @@ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- -Ran 5 tests in 0.074s +Ran 5 tests in 0.056s FAILED (errors=1) ... ---------------------------------------------------------------------- -Ran 3 tests in 0.057s +Ran 3 tests in 0.034s OK !!! TEST FAILURE: python UnitTestMolDescriptors.py {} @@ -31200,13 +31220,13 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 3 tests in 0.004s +Ran 3 tests in 0.003s FAILED (errors=3) !!! TEST FAILURE: python UnitTestCorrMatGen.py {} ...... ---------------------------------------------------------------------- -Ran 6 tests in 1.962s +Ran 6 tests in 0.769s OK ...EE.. @@ -31227,23 +31247,23 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 7 tests in 0.508s +Ran 7 tests in 0.172s FAILED (errors=2) !!! TEST FAILURE: python UnitTestPackage.py {} .... ---------------------------------------------------------------------- -Ran 4 tests in 0.052s +Ran 4 tests in 0.021s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 29.825s +Ran 5 tests in 6.279s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.034s +Ran 4 tests in 0.004s OK .... @@ -31253,7 +31273,7 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.050s +Ran 4 tests in 0.009s OK !!! TEST FAILURE: python UnitTestBuildComposite.py {} @@ -31265,73 +31285,97 @@ !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'} !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -200: [20:26:02] INFO: Reading molecules and constructing molecular database. +200: .........[07:12:03] INFO: Reading molecules and constructing molecular database. +200: +200: [07:12:03] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [07:12:03] INFO: Processing 10 molecules +200: +200: [07:12:03] INFO: Generating fingerprints and descriptors: +200: +200: [07:12:03] INFO: Finished. +200: +200: [07:12:04] INFO: Reading molecules and constructing molecular database. +200: +200: [07:12:04] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [07:12:04] INFO: Processing 10 molecules 200: -200: [20:26:02] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [07:12:04] INFO: Generating fingerprints and descriptors: 200: -200: [20:26:02] INFO: Processing 10 molecules +200: [07:12:04] INFO: Finished. 200: -200: [20:26:02] INFO: Generating fingerprints and descriptors: +200: [07:12:06] INFO: Reading molecules and constructing molecular database. 200: -200: [20:26:02] INFO: Finished. +200: [07:12:06] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [20:26:07] INFO: Reading molecules and constructing molecular database. +200: [07:12:06] INFO: Processing 10 molecules 200: -200: [20:26:07] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [07:12:06] INFO: Generating fingerprints and descriptors: 200: -200: [20:26:07] INFO: Generating fingerprints and descriptors: +200: [07:12:06] INFO: Finished. 200: -200: [20:26:07] INFO: Finished. +200: [07:12:07] INFO: Reading molecules and constructing molecular database. 200: -200: [20:26:12] INFO: Reading molecules and constructing molecular database. +200: [07:12:07] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [20:26:12] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [07:12:07] INFO: Generating fingerprints and descriptors: 200: -200: [20:26:12] INFO: Generating fingerprints and descriptors: +200: [07:12:07] INFO: Finished. 200: -200: [20:26:12] INFO: Finished. +200: [07:12:08] INFO: Reading molecules and constructing molecular database. 200: -200: .[20:26:17] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. +200: [07:12:08] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [20:26:17] INFO: Reading molecules and constructing molecular database. +200: [07:12:09] INFO: Generating fingerprints and descriptors: 200: -200: [20:26:17] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [07:12:09] INFO: Finished. 200: -200: [20:26:17] INFO: Processing 163 molecules +200: .[07:12:10] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 200: -200: [20:26:17] INFO: done 100 +200: [07:12:10] INFO: Reading molecules and constructing molecular database. 200: -200: [20:26:18] INFO: Generating fingerprints and descriptors: +200: [07:12:10] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [20:26:19] INFO: Finished. +200: [07:12:10] INFO: Processing 163 molecules 200: -200: .[20:26:29] INFO: Reading molecules and constructing molecular database. +200: [07:12:10] INFO: done 100 200: -200: [20:26:29] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [07:12:10] INFO: Generating fingerprints and descriptors: 200: -200: [20:26:29] INFO: Processing 10 molecules +200: [07:12:11] INFO: Finished. 200: -200: [20:26:29] INFO: Generating fingerprints and descriptors: +200: .[07:12:13] INFO: Reading molecules and constructing molecular database. 200: -200: [20:26:30] INFO: Finished. +200: [07:12:13] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 200: -200: [20:26:35] INFO: Reading molecules and constructing molecular database. +200: [07:12:13] INFO: Processing 10 molecules 200: -200: [20:26:35] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: [07:12:13] INFO: Generating fingerprints and descriptors: 200: -200: [20:26:35] INFO: Processing 10 molecules +200: [07:12:13] INFO: Finished. 200: -200: [20:26:35] INFO: Generating fingerprints and descriptors: +200: [07:12:15] INFO: Reading molecules and constructing molecular database. 200: -200: [20:26:35] INFO: Finished. +200: [07:12:15] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +200: +200: [07:12:15] INFO: Processing 10 molecules +200: +200: [07:12:15] INFO: Generating fingerprints and descriptors: +200: +200: [07:12:15] INFO: Finished. 200: 200: . 200: ---------------------------------------------------------------------- -200: Ran 12 tests in 150.174s +200: Ran 12 tests in 44.410s 200: 200: OK -205/208 Test #200: pythonTestDbCLI ........................ Passed 153.23 sec -123: [20:27:07] done +205/208 Test #200: pythonTestDbCLI ........................ Passed 45.47 sec +5: [07:12:31] Finished: testMultipleTimes() +5: [07:12:31] +5: ----------------------------------------- +206/208 Test #5: testConcurrentQueue .................... Passed 195.73 sec +123: [07:12:32] 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 @@ -31342,28 +31386,25 @@ 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 -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: ..................[20:28:02] WARNING: More than one matching pattern found - picking one +208: ..................[07:12:53] WARNING: More than one matching pattern found - picking one 208: -208: [20:28:02] WARNING: More than one matching pattern found - picking one +208: [07:12:53] WARNING: More than one matching pattern found - picking one 208: -208: .[20:28:02] WARNING: More than one matching pattern found - picking one +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: .[07:12:53] WARNING: More than one matching pattern found - picking one 208: 123: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 123: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 123: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 123: CC(=O)C[C@@]12CCC[C@H]1[C@@H]1CCC3=CC(=O)CC[C@@H]3[C@H]1CC2 -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 208: ... 208: ---------------------------------------------------------------------- -208: Ran 23 tests in 184.888s +208: Ran 23 tests in 67.176s 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'} -123: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O +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) @@ -31383,7 +31424,7 @@ 208: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations 208: 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 1.044s +208: Ran 8 tests in 0.270s 208: 208: FAILED (errors=1) 208: Traceback (most recent call last): @@ -31418,13 +31459,15 @@ 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 +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 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 -208: F..[20:28:39] WARNING: not removing hydrogen atom without neighbors -208: [20:28:39] WARNING: not removing hydrogen atom without neighbors -208: [20:28:39] WARNING: not removing hydrogen atom without neighbors -208: ....[20:28:39] WARNING: not removing hydrogen atom without neighbors +208: F..[07:13:08] WARNING: not removing hydrogen atom without neighbors +208: [07:13:08] WARNING: not removing hydrogen atom without neighbors +208: [07:13:08] WARNING: not removing hydrogen atom without neighbors +208: ....[07:13:08] WARNING: not removing hydrogen atom without neighbors 208: ...... 208: ====================================================================== 208: FAIL: testBadAtomHandling (__main__.TestCase.testBadAtomHandling) @@ -31481,48 +31524,48 @@ 208: AssertionError: SMILES: CCC; Descriptor: Ipc 208: 208: ---------------------------------------------------------------------- -208: Ran 14 tests in 17.321s +208: Ran 14 tests in 7.263s 208: 208: FAILED (failures=2) -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: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 6.435s +208: Ran 4 tests in 2.894s 208: 208: OK -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: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 208: ...... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 1.860s +208: Ran 6 tests in 0.784s 208: 208: OK -123: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 -123: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 +123: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 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({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C', 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({ 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: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 -123: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] +123: 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: .......s..s........ 208: ---------------------------------------------------------------------- -208: Ran 26 tests in 10.455s +208: Ran 26 tests in 4.881s 208: 208: OK (skipped=2) -123: [20:29:45] Molecule does not have explicit Hs. Consider calling AddHs() -206/208 Test #123: testDistGeomHelpers .................... Passed 666.99 sec -208: .............F[20:29:50] WARNING: More than one matching pattern found - picking one +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-] +208: .............F[07:13:42] WARNING: More than one matching pattern found - picking one 208: -208: [20:29:50] WARNING: More than one matching pattern found - picking one +208: [07:13:42] WARNING: More than one matching pattern found - picking one 208: -208: ..[20:29:51] Molecule does not have explicit Hs. Consider calling AddHs() -208: [20:29:51] Molecule does not have explicit Hs. Consider calling AddHs() -208: [20:29:51] Molecule does not have explicit Hs. Consider calling AddHs() -208: [20:29:51] Molecule does not have explicit Hs. Consider calling AddHs() +208: ..[07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() +208: [07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() +208: [07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() +208: [07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() +123: [07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() 208: ......... 208: ====================================================================== 208: FAIL: FindBRICSBonds (rdkit.Chem.BRICS) @@ -31551,270 +31594,271 @@ 208: 208: 208: ---------------------------------------------------------------------- -208: Ran 25 tests in 40.469s +208: Ran 25 tests in 19.686s 208: 208: FAILED (failures=1) +207/208 Test #123: testDistGeomHelpers .................... Passed 234.70 sec 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.523s +208: Ran 2 tests in 0.105s 208: 208: OK 208: ..s... 208: ---------------------------------------------------------------------- -208: Ran 6 tests in 4.577s +208: Ran 6 tests in 1.861s 208: 208: OK (skipped=1) -208: ..[20:30:01] WARNING: not removing hydrogen atom without neighbors -208: .[20:30:01] WARNING: not removing hydrogen atom without neighbors -208: .[20:30:01] WARNING: no name column found on line 1 -208: [20:30:01] WARNING: no name column found on line 2 -208: [20:30:01] WARNING: no name column found on line 3 -208: [20:30:01] WARNING: no name column found on line 4 -208: [20:30:01] WARNING: no name column found on line 5 -208: [20:30:01] WARNING: no name column found on line 6 -208: [20:30:01] WARNING: no name column found on line 7 -208: [20:30:01] WARNING: no name column found on line 8 -208: [20:30:01] WARNING: no name column found on line 9 -208: [20:30:01] WARNING: no name column found on line 10 -208: [20:30:01] WARNING: no name column found on line 11 -208: [20:30:01] WARNING: no name column found on line 12 -208: [20:30:01] WARNING: no name column found on line 13 -208: [20:30:01] WARNING: no name column found on line 14 -208: [20:30:01] WARNING: no name column found on line 15 -208: [20:30:01] WARNING: no name column found on line 16 -208: [20:30:01] WARNING: no name column found on line 17 -208: [20:30:01] WARNING: no name column found on line 18 -208: [20:30:01] WARNING: no name column found on line 19 -208: [20:30:01] WARNING: no name column found on line 20 -208: [20:30:01] WARNING: no name column found on line 21 -208: [20:30:01] WARNING: no name column found on line 22 -208: [20:30:01] WARNING: no name column found on line 23 -208: [20:30:01] WARNING: no name column found on line 24 -208: [20:30:01] WARNING: no name column found on line 25 -208: [20:30:01] WARNING: no name column found on line 26 -208: [20:30:01] WARNING: no name column found on line 27 -208: [20:30:01] WARNING: no name column found on line 28 -208: [20:30:01] WARNING: no name column found on line 29 -208: [20:30:01] WARNING: no name column found on line 30 -208: [20:30:01] WARNING: no name column found on line 31 -208: [20:30:01] WARNING: no name column found on line 32 -208: [20:30:01] WARNING: no name column found on line 33 -208: [20:30:01] WARNING: no name column found on line 34 -208: [20:30:01] WARNING: no name column found on line 35 -208: [20:30:01] WARNING: no name column found on line 36 -208: [20:30:01] WARNING: no name column found on line 37 -208: [20:30:01] WARNING: no name column found on line 38 -208: [20:30:01] WARNING: no name column found on line 39 -208: [20:30:01] WARNING: no name column found on line 40 -208: [20:30:01] WARNING: no name column found on line 41 -208: [20:30:01] WARNING: no name column found on line 42 -208: [20:30:01] WARNING: no name column found on line 43 -208: [20:30:01] WARNING: no name column found on line 44 -208: [20:30:01] WARNING: no name column found on line 45 -208: [20:30:01] WARNING: no name column found on line 46 -208: [20:30:01] WARNING: no name column found on line 47 -208: [20:30:01] WARNING: no name column found on line 48 -208: [20:30:01] WARNING: no name column found on line 49 -208: [20:30:01] WARNING: no name column found on line 50 -208: [20:30:01] WARNING: no name column found on line 51 -208: [20:30:01] WARNING: no name column found on line 52 -208: [20:30:01] WARNING: no name column found on line 53 -208: [20:30:01] WARNING: no name column found on line 54 -208: [20:30:01] WARNING: no name column found on line 55 -208: [20:30:01] WARNING: no name column found on line 56 -208: [20:30:01] WARNING: no name column found on line 57 -208: [20:30:01] WARNING: no name column found on line 58 -208: [20:30:01] WARNING: no name column found on line 59 -208: [20:30:01] WARNING: no name column found on line 60 -208: [20:30:01] WARNING: no name column found on line 61 -208: [20:30:01] WARNING: no name column found on line 62 -208: [20:30:01] WARNING: no name column found on line 63 -208: [20:30:01] WARNING: no name column found on line 64 -208: [20:30:01] WARNING: no name column found on line 65 -208: [20:30:01] WARNING: no name column found on line 66 -208: [20:30:01] WARNING: no name column found on line 67 -208: [20:30:01] WARNING: no name column found on line 68 -208: [20:30:01] WARNING: no name column found on line 69 -208: [20:30:01] WARNING: no name column found on line 70 -208: [20:30:01] WARNING: no name column found on line 71 -208: [20:30:01] WARNING: no name column found on line 72 -208: [20:30:01] WARNING: no name column found on line 73 -208: [20:30:01] WARNING: no name column found on line 74 -208: [20:30:01] WARNING: no name column found on line 75 -208: [20:30:01] WARNING: no name column found on line 76 -208: [20:30:01] WARNING: no name column found on line 77 -208: [20:30:01] WARNING: no name column found on line 78 -208: [20:30:01] WARNING: no name column found on line 79 -208: [20:30:01] WARNING: no name column found on line 80 -208: [20:30:01] WARNING: no name column found on line 81 -208: [20:30:01] WARNING: no name column found on line 82 -208: [20:30:01] WARNING: no name column found on line 83 -208: [20:30:01] WARNING: no name column found on line 84 -208: [20:30:01] WARNING: no name column found on line 85 -208: [20:30:01] WARNING: no name column found on line 86 -208: [20:30:01] WARNING: no name column found on line 87 -208: [20:30:01] WARNING: no name column found on line 88 -208: [20:30:01] WARNING: no name column found on line 89 -208: [20:30:01] WARNING: no name column found on line 90 -208: [20:30:01] WARNING: no name column found on line 91 -208: [20:30:01] WARNING: no name column found on line 92 -208: [20:30:01] WARNING: no name column found on line 93 -208: [20:30:01] WARNING: no name column found on line 94 -208: [20:30:01] WARNING: no name column found on line 95 -208: [20:30:01] WARNING: no name column found on line 96 -208: [20:30:01] WARNING: no name column found on line 97 -208: [20:30:01] WARNING: no name column found on line 98 -208: [20:30:01] WARNING: no name column found on line 99 -208: [20:30:01] WARNING: no name column found on line 100 -208: [20:30:01] WARNING: no name column found on line 101 -208: [20:30:01] WARNING: no name column found on line 102 -208: [20:30:01] WARNING: no name column found on line 103 -208: [20:30:01] WARNING: no name column found on line 104 -208: [20:30:01] WARNING: no name column found on line 105 -208: [20:30:01] WARNING: no name column found on line 106 -208: [20:30:01] WARNING: no name column found on line 107 -208: [20:30:01] WARNING: no name column found on line 108 -208: [20:30:01] WARNING: no name column found on line 109 -208: [20:30:01] WARNING: no name column found on line 110 -208: [20:30:01] WARNING: no name column found on line 111 -208: [20:30:01] WARNING: no name column found on line 112 -208: [20:30:01] WARNING: no name column found on line 113 -208: [20:30:01] WARNING: no name column found on line 114 -208: [20:30:01] WARNING: no name column found on line 115 -208: [20:30:01] WARNING: no name column found on line 116 -208: [20:30:01] WARNING: no name column found on line 117 -208: [20:30:01] WARNING: no name column found on line 118 -208: [20:30:01] WARNING: no name column found on line 119 -208: [20:30:01] WARNING: no name column found on line 120 -208: [20:30:01] WARNING: no name column found on line 121 -208: [20:30:01] WARNING: no name column found on line 122 -208: [20:30:01] WARNING: no name column found on line 123 -208: [20:30:01] WARNING: no name column found on line 124 -208: [20:30:01] WARNING: no name column found on line 125 -208: [20:30:01] WARNING: no name column found on line 126 -208: [20:30:01] WARNING: no name column found on line 127 -208: [20:30:01] WARNING: no name column found on line 128 -208: [20:30:01] WARNING: no name column found on line 129 -208: [20:30:01] WARNING: no name column found on line 130 -208: [20:30:01] WARNING: no name column found on line 131 -208: [20:30:01] WARNING: no name column found on line 132 -208: [20:30:01] WARNING: no name column found on line 133 -208: [20:30:01] WARNING: no name column found on line 134 -208: [20:30:01] WARNING: no name column found on line 135 -208: [20:30:01] WARNING: no name column found on line 136 -208: [20:30:01] WARNING: no name column found on line 137 -208: [20:30:01] WARNING: no name column found on line 138 -208: [20:30:01] WARNING: no name column found on line 139 -208: [20:30:01] WARNING: no name column found on line 140 -208: [20:30:01] WARNING: no name column found on line 141 -208: [20:30:01] WARNING: no name column found on line 142 -208: [20:30:01] WARNING: no name column found on line 143 -208: [20:30:01] WARNING: no name column found on line 144 -208: [20:30:01] WARNING: no name column found on line 145 -208: [20:30:01] WARNING: no name column found on line 146 -208: [20:30:01] WARNING: no name column found on line 147 -208: [20:30:01] WARNING: no name column found on line 148 -208: [20:30:01] WARNING: no name column found on line 149 -208: [20:30:01] WARNING: no name column found on line 150 -208: [20:30:01] WARNING: no name column found on line 151 -208: [20:30:01] WARNING: no name column found on line 152 -208: [20:30:01] WARNING: no name column found on line 153 -208: [20:30:01] WARNING: no name column found on line 154 -208: [20:30:01] WARNING: no name column found on line 155 -208: [20:30:01] WARNING: no name column found on line 156 -208: [20:30:01] WARNING: no name column found on line 157 -208: [20:30:01] WARNING: no name column found on line 158 -208: [20:30:01] WARNING: no name column found on line 159 -208: [20:30:01] WARNING: no name column found on line 160 -208: [20:30:01] WARNING: no name column found on line 161 -208: [20:30:01] WARNING: no name column found on line 162 -208: [20:30:01] WARNING: no name column found on line 163 -208: [20:30:01] WARNING: no name column found on line 164 -208: [20:30:01] WARNING: no name column found on line 165 -208: [20:30:01] WARNING: no name column found on line 166 -208: [20:30:01] WARNING: no name column found on line 167 -208: [20:30:01] WARNING: no name column found on line 168 -208: [20:30:01] WARNING: no name column found on line 169 -208: [20:30:01] WARNING: no name column found on line 170 -208: [20:30:01] WARNING: no name column found on line 171 -208: [20:30:01] WARNING: no name column found on line 172 -208: [20:30:01] WARNING: no name column found on line 173 -208: [20:30:01] WARNING: no name column found on line 174 -208: [20:30:01] WARNING: no name column found on line 175 -208: [20:30:01] WARNING: no name column found on line 176 -208: [20:30:01] WARNING: no name column found on line 177 -208: [20:30:01] WARNING: no name column found on line 178 -208: [20:30:01] WARNING: no name column found on line 179 -208: [20:30:01] WARNING: no name column found on line 180 -208: [20:30:01] WARNING: no name column found on line 181 -208: [20:30:01] WARNING: no name column found on line 182 -208: [20:30:01] WARNING: no name column found on line 183 -208: [20:30:01] WARNING: no name column found on line 184 -208: [20:30:01] WARNING: no name column found on line 185 -208: [20:30:01] WARNING: no name column found on line 186 -208: [20:30:01] WARNING: no name column found on line 187 -208: [20:30:01] WARNING: no name column found on line 188 -208: [20:30:01] WARNING: no name column found on line 189 -208: [20:30:01] WARNING: no name column found on line 190 -208: [20:30:01] WARNING: no name column found on line 191 -208: [20:30:01] WARNING: no name column found on line 192 -208: [20:30:01] WARNING: no name column found on line 193 -208: [20:30:01] WARNING: no name column found on line 194 -208: [20:30:01] WARNING: no name column found on line 195 -208: [20:30:01] WARNING: no name column found on line 196 -208: [20:30:01] WARNING: no name column found on line 197 -208: [20:30:01] WARNING: no name column found on line 198 -208: [20:30:01] WARNING: no name column found on line 199 -208: [20:30:01] WARNING: no name column found on line 200 -208: [20:30:01] WARNING: no name column found on line 201 -208: [20:30:01] WARNING: no name column found on line 202 -208: [20:30:01] WARNING: no name column found on line 203 -208: [20:30:01] WARNING: no name column found on line 204 -208: [20:30:01] WARNING: no name column found on line 205 -208: [20:30:01] WARNING: no name column found on line 206 -208: [20:30:01] WARNING: no name column found on line 207 -208: [20:30:01] WARNING: no name column found on line 208 -208: [20:30:01] WARNING: no name column found on line 209 -208: [20:30:01] WARNING: no name column found on line 210 -208: [20:30:01] WARNING: no name column found on line 211 -208: [20:30:01] WARNING: no name column found on line 212 -208: [20:30:01] WARNING: no name column found on line 213 -208: [20:30:01] WARNING: no name column found on line 214 -208: [20:30:01] WARNING: no name column found on line 215 -208: [20:30:01] WARNING: no name column found on line 216 +208: ..[07:13:46] WARNING: not removing hydrogen atom without neighbors +208: .[07:13:46] WARNING: not removing hydrogen atom without neighbors +208: .[07:13:46] WARNING: no name column found on line 1 +208: [07:13:46] WARNING: no name column found on line 2 +208: [07:13:46] WARNING: no name column found on line 3 +208: [07:13:46] WARNING: no name column found on line 4 +208: [07:13:46] WARNING: no name column found on line 5 +208: [07:13:46] WARNING: no name column found on line 6 +208: [07:13:46] WARNING: no name column found on line 7 +208: [07:13:46] WARNING: no name column found on line 8 +208: [07:13:46] WARNING: no name column found on line 9 +208: [07:13:46] WARNING: no name column found on line 10 +208: [07:13:46] WARNING: no name column found on line 11 +208: [07:13:46] WARNING: no name column found on line 12 +208: [07:13:46] WARNING: no name column found on line 13 +208: [07:13:46] WARNING: no name column found on line 14 +208: [07:13:46] WARNING: no name column found on line 15 +208: [07:13:46] WARNING: no name column found on line 16 +208: [07:13:46] WARNING: no name column found on line 17 +208: [07:13:46] WARNING: no name column found on line 18 +208: [07:13:46] WARNING: no name column found on line 19 +208: [07:13:46] WARNING: no name column found on line 20 +208: [07:13:46] WARNING: no name column found on line 21 +208: [07:13:46] WARNING: no name column found on line 22 +208: [07:13:46] WARNING: no name column found on line 23 +208: [07:13:46] WARNING: no name column found on line 24 +208: [07:13:46] WARNING: no name column found on line 25 +208: [07:13:46] WARNING: no name column found on line 26 +208: [07:13:46] WARNING: no name column found on line 27 +208: [07:13:46] WARNING: no name column found on line 28 +208: [07:13:46] WARNING: no name column found on line 29 +208: [07:13:46] WARNING: no name column found on line 30 +208: [07:13:46] WARNING: no name column found on line 31 +208: [07:13:46] WARNING: no name column found on line 32 +208: [07:13:46] WARNING: no name column found on line 33 +208: [07:13:46] WARNING: no name column found on line 34 +208: [07:13:46] WARNING: no name column found on line 35 +208: [07:13:46] WARNING: no name column found on line 36 +208: [07:13:46] WARNING: no name column found on line 37 +208: [07:13:46] WARNING: no name column found on line 38 +208: [07:13:46] WARNING: no name column found on line 39 +208: [07:13:46] WARNING: no name column found on line 40 +208: [07:13:46] WARNING: no name column found on line 41 +208: [07:13:46] WARNING: no name column found on line 42 +208: [07:13:46] WARNING: no name column found on line 43 +208: [07:13:46] WARNING: no name column found on line 44 +208: [07:13:46] WARNING: no name column found on line 45 +208: [07:13:46] WARNING: no name column found on line 46 +208: [07:13:46] WARNING: no name column found on line 47 +208: [07:13:46] WARNING: no name column found on line 48 +208: [07:13:46] WARNING: no name column found on line 49 +208: [07:13:46] WARNING: no name column found on line 50 +208: [07:13:46] WARNING: no name column found on line 51 +208: [07:13:46] WARNING: no name column found on line 52 +208: [07:13:46] WARNING: no name column found on line 53 +208: [07:13:46] WARNING: no name column found on line 54 +208: [07:13:46] WARNING: no name column found on line 55 +208: [07:13:46] WARNING: no name column found on line 56 +208: [07:13:46] WARNING: no name column found on line 57 +208: [07:13:46] WARNING: no name column found on line 58 +208: [07:13:46] WARNING: no name column found on line 59 +208: [07:13:46] WARNING: no name column found on line 60 +208: [07:13:46] WARNING: no name column found on line 61 +208: [07:13:46] WARNING: no name column found on line 62 +208: [07:13:46] WARNING: no name column found on line 63 +208: [07:13:46] WARNING: no name column found on line 64 +208: [07:13:46] WARNING: no name column found on line 65 +208: [07:13:46] WARNING: no name column found on line 66 +208: [07:13:46] WARNING: no name column found on line 67 +208: [07:13:46] WARNING: no name column found on line 68 +208: [07:13:46] WARNING: no name column found on line 69 +208: [07:13:46] WARNING: no name column found on line 70 +208: [07:13:46] WARNING: no name column found on line 71 +208: [07:13:46] WARNING: no name column found on line 72 +208: [07:13:46] WARNING: no name column found on line 73 +208: [07:13:46] WARNING: no name column found on line 74 +208: [07:13:46] WARNING: no name column found on line 75 +208: [07:13:46] WARNING: no name column found on line 76 +208: [07:13:46] WARNING: no name column found on line 77 +208: [07:13:46] WARNING: no name column found on line 78 +208: [07:13:46] WARNING: no name column found on line 79 +208: [07:13:46] WARNING: no name column found on line 80 +208: [07:13:46] WARNING: no name column found on line 81 +208: [07:13:46] WARNING: no name column found on line 82 +208: [07:13:46] WARNING: no name column found on line 83 +208: [07:13:46] WARNING: no name column found on line 84 +208: [07:13:46] WARNING: no name column found on line 85 +208: [07:13:46] WARNING: no name column found on line 86 +208: [07:13:46] WARNING: no name column found on line 87 +208: [07:13:46] WARNING: no name column found on line 88 +208: [07:13:46] WARNING: no name column found on line 89 +208: [07:13:46] WARNING: no name column found on line 90 +208: [07:13:46] WARNING: no name column found on line 91 +208: [07:13:46] WARNING: no name column found on line 92 +208: [07:13:46] WARNING: no name column found on line 93 +208: [07:13:46] WARNING: no name column found on line 94 +208: [07:13:46] WARNING: no name column found on line 95 +208: [07:13:46] WARNING: no name column found on line 96 +208: [07:13:46] WARNING: no name column found on line 97 +208: [07:13:46] WARNING: no name column found on line 98 +208: [07:13:46] WARNING: no name column found on line 99 +208: [07:13:46] WARNING: no name column found on line 100 +208: [07:13:46] WARNING: no name column found on line 101 +208: [07:13:46] WARNING: no name column found on line 102 +208: [07:13:46] WARNING: no name column found on line 103 +208: [07:13:46] WARNING: no name column found on line 104 +208: [07:13:46] WARNING: no name column found on line 105 +208: [07:13:46] WARNING: no name column found on line 106 +208: [07:13:46] WARNING: no name column found on line 107 +208: [07:13:46] WARNING: no name column found on line 108 +208: [07:13:46] WARNING: no name column found on line 109 +208: [07:13:46] WARNING: no name column found on line 110 +208: [07:13:46] WARNING: no name column found on line 111 +208: [07:13:46] WARNING: no name column found on line 112 +208: [07:13:46] WARNING: no name column found on line 113 +208: [07:13:46] WARNING: no name column found on line 114 +208: [07:13:46] WARNING: no name column found on line 115 +208: [07:13:46] WARNING: no name column found on line 116 +208: [07:13:46] WARNING: no name column found on line 117 +208: [07:13:46] WARNING: no name column found on line 118 +208: [07:13:46] WARNING: no name column found on line 119 +208: [07:13:46] WARNING: no name column found on line 120 +208: [07:13:46] WARNING: no name column found on line 121 +208: [07:13:46] WARNING: no name column found on line 122 +208: [07:13:46] WARNING: no name column found on line 123 +208: [07:13:46] WARNING: no name column found on line 124 +208: [07:13:46] WARNING: no name column found on line 125 +208: [07:13:46] WARNING: no name column found on line 126 +208: [07:13:46] WARNING: no name column found on line 127 +208: [07:13:46] WARNING: no name column found on line 128 +208: [07:13:46] WARNING: no name column found on line 129 +208: [07:13:46] WARNING: no name column found on line 130 +208: [07:13:46] WARNING: no name column found on line 131 +208: [07:13:46] WARNING: no name column found on line 132 +208: [07:13:46] WARNING: no name column found on line 133 +208: [07:13:46] WARNING: no name column found on line 134 +208: [07:13:46] WARNING: no name column found on line 135 +208: [07:13:46] WARNING: no name column found on line 136 +208: [07:13:46] WARNING: no name column found on line 137 +208: [07:13:46] WARNING: no name column found on line 138 +208: [07:13:46] WARNING: no name column found on line 139 +208: [07:13:46] WARNING: no name column found on line 140 +208: [07:13:46] WARNING: no name column found on line 141 +208: [07:13:46] WARNING: no name column found on line 142 +208: [07:13:46] WARNING: no name column found on line 143 +208: [07:13:46] WARNING: no name column found on line 144 +208: [07:13:46] WARNING: no name column found on line 145 +208: [07:13:46] WARNING: no name column found on line 146 +208: [07:13:46] WARNING: no name column found on line 147 +208: [07:13:46] WARNING: no name column found on line 148 +208: [07:13:46] WARNING: no name column found on line 149 +208: [07:13:46] WARNING: no name column found on line 150 +208: [07:13:46] WARNING: no name column found on line 151 +208: [07:13:46] WARNING: no name column found on line 152 +208: [07:13:46] WARNING: no name column found on line 153 +208: [07:13:46] WARNING: no name column found on line 154 +208: [07:13:46] WARNING: no name column found on line 155 +208: [07:13:46] WARNING: no name column found on line 156 +208: [07:13:46] WARNING: no name column found on line 157 +208: [07:13:46] WARNING: no name column found on line 158 +208: [07:13:46] WARNING: no name column found on line 159 +208: [07:13:46] WARNING: no name column found on line 160 +208: [07:13:46] WARNING: no name column found on line 161 +208: [07:13:46] WARNING: no name column found on line 162 +208: [07:13:46] WARNING: no name column found on line 163 +208: [07:13:46] WARNING: no name column found on line 164 +208: [07:13:46] WARNING: no name column found on line 165 +208: [07:13:46] WARNING: no name column found on line 166 +208: [07:13:46] WARNING: no name column found on line 167 +208: [07:13:46] WARNING: no name column found on line 168 +208: [07:13:46] WARNING: no name column found on line 169 +208: [07:13:46] WARNING: no name column found on line 170 +208: [07:13:46] WARNING: no name column found on line 171 +208: [07:13:46] WARNING: no name column found on line 172 +208: [07:13:46] WARNING: no name column found on line 173 +208: [07:13:46] WARNING: no name column found on line 174 +208: [07:13:46] WARNING: no name column found on line 175 +208: [07:13:46] WARNING: no name column found on line 176 +208: [07:13:46] WARNING: no name column found on line 177 +208: [07:13:46] WARNING: no name column found on line 178 +208: [07:13:46] WARNING: no name column found on line 179 +208: [07:13:46] WARNING: no name column found on line 180 +208: [07:13:46] WARNING: no name column found on line 181 +208: [07:13:46] WARNING: no name column found on line 182 +208: [07:13:46] WARNING: no name column found on line 183 +208: [07:13:46] WARNING: no name column found on line 184 +208: [07:13:46] WARNING: no name column found on line 185 +208: [07:13:46] WARNING: no name column found on line 186 +208: [07:13:46] WARNING: no name column found on line 187 +208: [07:13:46] WARNING: no name column found on line 188 +208: [07:13:46] WARNING: no name column found on line 189 +208: [07:13:46] WARNING: no name column found on line 190 +208: [07:13:46] WARNING: no name column found on line 191 +208: [07:13:46] WARNING: no name column found on line 192 +208: [07:13:46] WARNING: no name column found on line 193 +208: [07:13:46] WARNING: no name column found on line 194 +208: [07:13:46] WARNING: no name column found on line 195 +208: [07:13:46] WARNING: no name column found on line 196 +208: [07:13:46] WARNING: no name column found on line 197 +208: [07:13:46] WARNING: no name column found on line 198 +208: [07:13:46] WARNING: no name column found on line 199 +208: [07:13:46] WARNING: no name column found on line 200 +208: [07:13:46] WARNING: no name column found on line 201 +208: [07:13:46] WARNING: no name column found on line 202 +208: [07:13:46] WARNING: no name column found on line 203 +208: [07:13:46] WARNING: no name column found on line 204 +208: [07:13:46] WARNING: no name column found on line 205 +208: [07:13:46] WARNING: no name column found on line 206 +208: [07:13:46] WARNING: no name column found on line 207 +208: [07:13:46] WARNING: no name column found on line 208 +208: [07:13:46] WARNING: no name column found on line 209 +208: [07:13:46] WARNING: no name column found on line 210 +208: [07:13:46] WARNING: no name column found on line 211 +208: [07:13:46] WARNING: no name column found on line 212 +208: [07:13:46] WARNING: no name column found on line 213 +208: [07:13:46] WARNING: no name column found on line 214 +208: [07:13:46] WARNING: no name column found on line 215 +208: [07:13:46] WARNING: no name column found on line 216 208: ...... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.352s +208: Ran 10 tests in 0.289s 208: 208: OK 208: .................. 208: ---------------------------------------------------------------------- -208: Ran 18 tests in 3.409s +208: Ran 18 tests in 1.653s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.207s +208: Ran 3 tests in 0.190s 208: 208: OK 208: ........ 208: ---------------------------------------------------------------------- -208: Ran 8 tests in 0.158s +208: Ran 8 tests in 0.062s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.070s +208: Ran 2 tests in 0.050s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.053s +208: Ran 2 tests in 0.035s 208: 208: OK 208: . 208: ---------------------------------------------------------------------- -208: Ran 1 test in 0.314s +208: Ran 1 test in 0.182s 208: 208: OK 208: ........ @@ -31824,12 +31868,12 @@ 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.015s +208: Ran 3 tests in 0.011s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.004s +208: Ran 3 tests in 0.003s 208: 208: OK 208: ...E @@ -31851,28 +31895,28 @@ 208: RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) 208: 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.022s +208: Ran 4 tests in 0.013s 208: 208: FAILED (errors=1) 208: !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} 208: ....... 208: ---------------------------------------------------------------------- -208: Ran 7 tests in 0.126s +208: Ran 7 tests in 0.032s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.052s +208: Ran 4 tests in 0.033s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 12.180s +208: Ran 4 tests in 5.645s 208: 208: OK 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.203s +208: Ran 10 tests in 0.099s 208: 208: OK 208: . @@ -31882,7 +31926,7 @@ 208: OK 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 0.035s +208: Ran 10 tests in 0.009s 208: 208: OK 208: ....E @@ -31901,15 +31945,15 @@ 208: TypeError: Random.shuffle() got an unexpected keyword argument 'random' 208: 208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.216s +208: Ran 5 tests in 0.090s 208: 208: FAILED (errors=1) 208: !!! TEST FAILURE: python UnitTestGobbi.py {} -208: ................[20:31:12] Molecule does not have explicit Hs. Consider calling AddHs() -208: [20:31:12] Molecule does not have explicit Hs. Consider calling AddHs() +208: ................[07:14:20] Molecule does not have explicit Hs. Consider calling AddHs() +208: [07:14:20] Molecule does not have explicit Hs. Consider calling AddHs() 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 21 tests in 22.772s +208: Ran 21 tests in 10.935s 208: 208: OK 208: mol_197 @@ -31923,7 +31967,7 @@ 208: Ran 1 test in 0.001s 208: 208: OK -208: ...[20:31:15] +208: ...[07:14:21] 208: 208: **** 208: Pre-condition Violation @@ -31934,65 +31978,65 @@ 208: 208: . 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.127s +208: Ran 4 tests in 0.050s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 32.760s +208: Ran 2 tests in 16.404s 208: 208: OK 208: .. 208: ---------------------------------------------------------------------- -208: Ran 2 tests in 0.285s +208: Ran 2 tests in 0.199s 208: 208: OK 208: ... 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.039s +208: Ran 3 tests in 0.024s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.074s +208: Ran 4 tests in 0.050s 208: 208: OK -208: .....[20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors -208: [20:31:58] WARNING: not removing hydrogen atom without neighbors +208: .....[07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors +208: [07:14:43] WARNING: not removing hydrogen atom without neighbors 208: ..... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 1.081s +208: Ran 10 tests in 0.785s 208: 208: OK -208: ssssss[20:32:02] No suitable metadata found. -208: .[20:32:02] No suitable metadata found. +208: ssssss[07:14:44] No suitable metadata found. +208: .[07:14:44] No suitable metadata found. 208: ......s/build/rdkit-202209.3/obj-aarch64-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 2.496s +208: Ran 19 tests in 0.918s 208: 208: OK (skipped=7) 208: sss. 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 3.690s +208: Ran 4 tests in 1.761s 208: 208: OK (skipped=3) 208: sss @@ -32002,33 +32046,33 @@ 208: OK (skipped=3) 208: .......... 208: ---------------------------------------------------------------------- -208: Ran 10 tests in 2.599s +208: Ran 10 tests in 1.259s 208: 208: OK -208: ..[20:32:17] SMARTS Parse Error: syntax error while parsing: boromicacid -208: [20:32:17] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -208: [20:32:17] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -208: [20:32:17] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -208: [20:32:17] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -208: [20:32:17] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -208: [20:32:17] reaction has no reactants -208: [20:32:17] reaction has no products -208: [20:32:17] initialization failed -208: [20:32:17] reaction has no reactants -208: [20:32:17] reaction has no products +208: ..[07:14:52] SMARTS Parse Error: syntax error while parsing: boromicacid +208: [07:14:52] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +208: [07:14:52] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +208: [07:14:52] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +208: [07:14:52] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +208: [07:14:52] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +208: [07:14:52] reaction has no reactants +208: [07:14:52] reaction has no products +208: [07:14:52] initialization failed +208: [07:14:52] reaction has no reactants +208: [07:14:52] reaction has no products 208: . 208: ---------------------------------------------------------------------- -208: Ran 3 tests in 0.074s +208: Ran 3 tests in 0.066s 208: 208: OK 208: .... 208: ---------------------------------------------------------------------- -208: Ran 4 tests in 0.035s +208: Ran 4 tests in 0.022s 208: 208: OK 208: .................... 208: ---------------------------------------------------------------------- -208: Ran 20 tests in 0.543s +208: Ran 20 tests in 0.219s 208: 208: OK 208: !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} @@ -32037,18 +32081,18 @@ 208: !!! TEST FAILURE: python UnitTestDocTestsChem.py {} 208: !!! TEST FAILURE: python test_list.py {'dir': 'FeatMaps'} 208: !!! TEST FAILURE: python test_list.py {'dir': 'Pharm2D'} -207/208 Test #208: pythonTestDirChem ......................***Failed 480.26 sec +208/208 Test #208: pythonTestDirChem ......................***Failed 197.19 sec ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.667s +Ran 7 tests in 0.185s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.470s +Ran 6 tests in 0.082s OK -....[20:24:35] +....[07:11:40] **** Pre-condition Violation @@ -32059,22 +32103,22 @@ . ---------------------------------------------------------------------- -Ran 5 tests in 0.088s +Ran 5 tests in 0.019s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.088s +Ran 4 tests in 0.023s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.090s +Ran 2 tests in 0.019s OK ...................... ---------------------------------------------------------------------- -Ran 22 tests in 0.264s +Ran 22 tests in 0.063s OK .....s..........E......ss @@ -32099,60 +32143,60 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 25 tests in 0.745s +Ran 25 tests in 0.279s FAILED (errors=1, skipped=3) ..s ---------------------------------------------------------------------- -Ran 3 tests in 1.011s +Ran 3 tests in 0.315s OK (skipped=1) ................................... ---------------------------------------------------------------------- -Ran 35 tests in 1.235s +Ran 35 tests in 1.097s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.121s +Ran 4 tests in 0.087s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.099s +Ran 1 test in 0.022s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.247s +Ran 7 tests in 0.155s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.250s +Ran 3 tests in 0.096s OK .ss.ss....... ---------------------------------------------------------------------- -Ran 13 tests in 7.608s +Ran 13 tests in 2.407s OK (skipped=4) -[20:25:14] Molecule does not have explicit Hs. Consider calling AddHs() -.[20:25:14] Molecule does not have explicit Hs. Consider calling AddHs() -..................[20:28:02] WARNING: More than one matching pattern found - picking one +[07:11:52] Molecule does not have explicit Hs. Consider calling AddHs() +.[07:11:52] Molecule does not have explicit Hs. Consider calling AddHs() +..................[07:12:53] WARNING: More than one matching pattern found - picking one -[20:28:02] WARNING: More than one matching pattern found - picking one +[07:12:53] WARNING: More than one matching pattern found - picking one -.[20:28:02] WARNING: More than one matching pattern found - picking one +.[07:12:53] WARNING: More than one matching pattern found - picking one ... ---------------------------------------------------------------------- -Ran 23 tests in 184.888s +Ran 23 tests in 67.176s 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) @@ -32172,7 +32216,7 @@ https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations ---------------------------------------------------------------------- -Ran 8 tests in 1.044s +Ran 8 tests in 0.270s FAILED (errors=1) Traceback (most recent call last): @@ -32207,10 +32251,10 @@ `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..[20:28:39] WARNING: not removing hydrogen atom without neighbors -[20:28:39] WARNING: not removing hydrogen atom without neighbors -[20:28:39] WARNING: not removing hydrogen atom without neighbors -....[20:28:39] WARNING: not removing hydrogen atom without neighbors +F..[07:13:08] WARNING: not removing hydrogen atom without neighbors +[07:13:08] WARNING: not removing hydrogen atom without neighbors +[07:13:08] WARNING: not removing hydrogen atom without neighbors +....[07:13:08] WARNING: not removing hydrogen atom without neighbors ...... ====================================================================== FAIL: testBadAtomHandling (__main__.TestCase.testBadAtomHandling) @@ -32267,17 +32311,17 @@ AssertionError: SMILES: CCC; Descriptor: Ipc ---------------------------------------------------------------------- -Ran 14 tests in 17.321s +Ran 14 tests in 7.263s FAILED (failures=2) .... ---------------------------------------------------------------------- -Ran 4 tests in 6.435s +Ran 4 tests in 2.894s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 1.860s +Ran 6 tests in 0.784s OK .......:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead. @@ -32288,17 +32332,17 @@ antibiotics = antibiotics.append({ .......s..s........ ---------------------------------------------------------------------- -Ran 26 tests in 10.455s +Ran 26 tests in 4.881s OK (skipped=2) -.............F[20:29:50] WARNING: More than one matching pattern found - picking one +.............F[07:13:42] WARNING: More than one matching pattern found - picking one -[20:29:50] WARNING: More than one matching pattern found - picking one +[07:13:42] WARNING: More than one matching pattern found - picking one -..[20:29:51] Molecule does not have explicit Hs. Consider calling AddHs() -[20:29:51] Molecule does not have explicit Hs. Consider calling AddHs() -[20:29:51] Molecule does not have explicit Hs. Consider calling AddHs() -[20:29:51] Molecule does not have explicit Hs. Consider calling AddHs() +..[07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() +[07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() +[07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() +[07:13:42] Molecule does not have explicit Hs. Consider calling AddHs() ......... ====================================================================== FAIL: FindBRICSBonds (rdkit.Chem.BRICS) @@ -32327,270 +32371,270 @@ ---------------------------------------------------------------------- -Ran 25 tests in 40.469s +Ran 25 tests in 19.686s FAILED (failures=1) .. ---------------------------------------------------------------------- -Ran 2 tests in 0.523s +Ran 2 tests in 0.105s OK ..s... ---------------------------------------------------------------------- -Ran 6 tests in 4.577s +Ran 6 tests in 1.861s OK (skipped=1) -..[20:30:01] WARNING: not removing hydrogen atom without neighbors -.[20:30:01] WARNING: not removing hydrogen atom without neighbors -.[20:30:01] WARNING: no name column found on line 1 -[20:30:01] WARNING: no name column found on line 2 -[20:30:01] WARNING: no name column found on line 3 -[20:30:01] WARNING: no name column found on line 4 -[20:30:01] WARNING: no name column found on line 5 -[20:30:01] WARNING: no name column found on line 6 -[20:30:01] WARNING: no name column found on line 7 -[20:30:01] WARNING: no name column found on line 8 -[20:30:01] WARNING: no name column found on line 9 -[20:30:01] WARNING: no name column found on line 10 -[20:30:01] WARNING: no name column found on line 11 -[20:30:01] WARNING: no name column found on line 12 -[20:30:01] WARNING: no name column found on line 13 -[20:30:01] WARNING: no name column found on line 14 -[20:30:01] WARNING: no name column found on line 15 -[20:30:01] WARNING: no name column found on line 16 -[20:30:01] WARNING: no name column found on line 17 -[20:30:01] WARNING: no name column found on line 18 -[20:30:01] WARNING: no name column found on line 19 -[20:30:01] WARNING: no name column found on line 20 -[20:30:01] WARNING: no name column found on line 21 -[20:30:01] WARNING: no name column found on line 22 -[20:30:01] WARNING: no name column found on line 23 -[20:30:01] WARNING: no name column found on line 24 -[20:30:01] WARNING: no name column found on line 25 -[20:30:01] WARNING: no name column found on line 26 -[20:30:01] WARNING: no name column found on line 27 -[20:30:01] WARNING: no name column found on line 28 -[20:30:01] WARNING: no name column found on line 29 -[20:30:01] WARNING: no name column found on line 30 -[20:30:01] WARNING: no name column found on line 31 -[20:30:01] WARNING: no name column found on line 32 -[20:30:01] WARNING: no name column found on line 33 -[20:30:01] WARNING: no name column found on line 34 -[20:30:01] WARNING: no name column found on line 35 -[20:30:01] WARNING: no name column found on line 36 -[20:30:01] WARNING: no name column found on line 37 -[20:30:01] WARNING: no name column found on line 38 -[20:30:01] WARNING: no name column found on line 39 -[20:30:01] WARNING: no name column found on line 40 -[20:30:01] WARNING: no name column found on line 41 -[20:30:01] WARNING: no name column found on line 42 -[20:30:01] WARNING: no name column found on line 43 -[20:30:01] 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-[20:30:01] WARNING: no name column found on line 63 -[20:30:01] WARNING: no name column found on line 64 -[20:30:01] WARNING: no name column found on line 65 -[20:30:01] WARNING: no name column found on line 66 -[20:30:01] WARNING: no name column found on line 67 -[20:30:01] WARNING: no name column found on line 68 -[20:30:01] WARNING: no name column found on line 69 -[20:30:01] WARNING: no name column found on line 70 -[20:30:01] WARNING: no name column found on line 71 -[20:30:01] WARNING: no name column found on line 72 -[20:30:01] WARNING: no name column found on line 73 -[20:30:01] WARNING: no name column found on line 74 -[20:30:01] WARNING: no name column found on line 75 -[20:30:01] WARNING: no name column found on line 76 -[20:30:01] WARNING: no name column found on line 77 -[20:30:01] WARNING: no name column found on line 78 -[20:30:01] WARNING: no name column found on line 79 -[20:30:01] WARNING: no name column found on line 80 -[20:30:01] WARNING: no name column found on line 81 -[20:30:01] WARNING: no name column found on line 82 -[20:30:01] WARNING: no name column found on line 83 -[20:30:01] WARNING: no name column found on line 84 -[20:30:01] WARNING: no name column found on line 85 -[20:30:01] WARNING: no name column found on line 86 -[20:30:01] WARNING: no name column found on line 87 -[20:30:01] WARNING: no name column found on line 88 -[20:30:01] WARNING: no name column found on line 89 -[20:30:01] WARNING: no name column found on line 90 -[20:30:01] WARNING: no name column found on line 91 -[20:30:01] WARNING: no name column found on line 92 -[20:30:01] WARNING: no name column found on line 93 -[20:30:01] WARNING: no name column found on line 94 -[20:30:01] WARNING: no name column found on line 95 -[20:30:01] WARNING: no name column found on line 96 -[20:30:01] WARNING: no name column found on line 97 -[20:30:01] WARNING: no name column found on line 98 -[20:30:01] WARNING: no name column found on line 99 -[20:30:01] WARNING: no name column found on line 100 -[20:30:01] WARNING: no name column found on line 101 -[20:30:01] WARNING: no name column found on line 102 -[20:30:01] WARNING: no name column found on line 103 -[20:30:01] WARNING: no name column found on line 104 -[20:30:01] WARNING: no name column found on line 105 -[20:30:01] WARNING: no name column found on line 106 -[20:30:01] WARNING: no name column found on line 107 -[20:30:01] WARNING: no name column found on line 108 -[20:30:01] WARNING: no name column found on line 109 -[20:30:01] WARNING: no name column found on line 110 -[20:30:01] WARNING: no name column found on line 111 -[20:30:01] WARNING: no name column found on line 112 -[20:30:01] WARNING: no name column found on line 113 -[20:30:01] WARNING: no name column found on line 114 -[20:30:01] WARNING: no name column found on line 115 -[20:30:01] WARNING: no name column found on line 116 -[20:30:01] WARNING: no name column found on line 117 -[20:30:01] WARNING: no name column found on line 118 -[20:30:01] WARNING: no name column found on line 119 -[20:30:01] WARNING: no name column found on line 120 -[20:30:01] WARNING: no name column found on line 121 -[20:30:01] WARNING: no name column found on line 122 -[20:30:01] WARNING: no name column found on line 123 -[20:30:01] WARNING: no name column found on line 124 -[20:30:01] WARNING: no name column found on line 125 -[20:30:01] WARNING: no name column found on line 126 -[20:30:01] WARNING: no name column found on line 127 -[20:30:01] WARNING: no name column found on line 128 -[20:30:01] WARNING: no name column found on line 129 -[20:30:01] WARNING: no name column found on line 130 -[20:30:01] WARNING: no name column found on line 131 -[20:30:01] WARNING: no name column found on line 132 -[20:30:01] WARNING: no name column found on line 133 -[20:30:01] WARNING: no name column found on line 134 -[20:30:01] WARNING: no name column found on line 135 -[20:30:01] WARNING: no name column found on line 136 -[20:30:01] WARNING: no name column found on line 137 -[20:30:01] WARNING: no name column found on line 138 -[20:30:01] WARNING: no name column found on line 139 -[20:30:01] WARNING: no name column found on line 140 -[20:30:01] WARNING: no name column found on line 141 -[20:30:01] WARNING: no name column found on line 142 -[20:30:01] WARNING: no name column found on line 143 -[20:30:01] WARNING: no name column found on line 144 -[20:30:01] WARNING: no name column found on line 145 -[20:30:01] WARNING: no name column found on line 146 -[20:30:01] WARNING: no name column found on line 147 -[20:30:01] WARNING: no name column found on line 148 -[20:30:01] WARNING: no name column found on line 149 -[20:30:01] WARNING: no name column found on line 150 -[20:30:01] WARNING: no name column found on line 151 -[20:30:01] WARNING: no name column found on line 152 -[20:30:01] WARNING: no name column found on line 153 -[20:30:01] WARNING: no name column found on line 154 -[20:30:01] WARNING: no name column found on line 155 -[20:30:01] WARNING: no name column found on line 156 -[20:30:01] WARNING: no name column found on line 157 -[20:30:01] WARNING: no name column found on line 158 -[20:30:01] WARNING: no name column found on line 159 -[20:30:01] WARNING: no name column found on line 160 -[20:30:01] WARNING: no name column found on line 161 -[20:30:01] WARNING: no name column found on line 162 -[20:30:01] WARNING: no name column found on line 163 -[20:30:01] WARNING: no name column found on line 164 -[20:30:01] WARNING: no name column found on line 165 -[20:30:01] WARNING: no name column found on line 166 -[20:30:01] WARNING: no name column found on line 167 -[20:30:01] WARNING: no name column found on line 168 -[20:30:01] WARNING: no name column found on line 169 -[20:30:01] WARNING: no name column found on line 170 -[20:30:01] WARNING: no name column found on line 171 -[20:30:01] WARNING: no name column found on line 172 -[20:30:01] WARNING: no name column found on line 173 -[20:30:01] WARNING: no name column found on line 174 -[20:30:01] WARNING: no name column found on line 175 -[20:30:01] WARNING: no name column found on line 176 -[20:30:01] WARNING: no name column found on line 177 -[20:30:01] WARNING: no name column found on line 178 -[20:30:01] WARNING: no name column found on line 179 -[20:30:01] WARNING: no name column found on line 180 -[20:30:01] WARNING: no name column found on line 181 -[20:30:01] WARNING: no name column found on line 182 -[20:30:01] WARNING: no name column found on line 183 -[20:30:01] WARNING: no name column found on line 184 -[20:30:01] WARNING: no name column found on line 185 -[20:30:01] WARNING: no name column found on line 186 -[20:30:01] WARNING: no name column found on line 187 -[20:30:01] WARNING: no name column found on line 188 -[20:30:01] WARNING: no name column found on line 189 -[20:30:01] WARNING: no name column found on line 190 -[20:30:01] WARNING: no name column found on line 191 -[20:30:01] WARNING: no name column found on line 192 -[20:30:01] WARNING: no name column found on line 193 -[20:30:01] WARNING: no name column found on line 194 -[20:30:01] WARNING: no name column found on line 195 -[20:30:01] WARNING: no name column found on line 196 -[20:30:01] WARNING: no name column found on line 197 -[20:30:01] WARNING: no name column found on line 198 -[20:30:01] WARNING: no name column found on line 199 -[20:30:01] WARNING: no name column found on line 200 -[20:30:01] WARNING: no name column found on line 201 -[20:30:01] WARNING: no name column found on line 202 -[20:30:01] WARNING: no name column found on line 203 -[20:30:01] WARNING: no name column found on line 204 -[20:30:01] WARNING: no name column found on line 205 -[20:30:01] WARNING: no name column found on line 206 -[20:30:01] WARNING: no name column found on line 207 -[20:30:01] WARNING: no name column found on line 208 -[20:30:01] WARNING: no name column found on line 209 -[20:30:01] WARNING: no name column found on line 210 -[20:30:01] WARNING: no name column found on line 211 -[20:30:01] WARNING: no name column found on line 212 -[20:30:01] WARNING: no name column found on line 213 -[20:30:01] WARNING: no name column found on line 214 -[20:30:01] WARNING: no name column found on line 215 -[20:30:01] WARNING: no name column found on line 216 +..[07:13:46] WARNING: not removing hydrogen atom without neighbors +.[07:13:46] WARNING: not removing hydrogen atom without neighbors +.[07:13:46] WARNING: no name column found on line 1 +[07:13:46] WARNING: no name column found on line 2 +[07:13:46] WARNING: no name column found on line 3 +[07:13:46] WARNING: no name column found on line 4 +[07:13:46] WARNING: no name column found on line 5 +[07:13:46] WARNING: no name column found on line 6 +[07:13:46] WARNING: no name column found on line 7 +[07:13:46] WARNING: no name column found on line 8 +[07:13:46] WARNING: no name column found on line 9 +[07:13:46] WARNING: no name column found on line 10 +[07:13:46] WARNING: no name column found on line 11 +[07:13:46] WARNING: no name column found on line 12 +[07:13:46] WARNING: no name column found on line 13 +[07:13:46] WARNING: no name column found on line 14 +[07:13:46] WARNING: no name column found on line 15 +[07:13:46] WARNING: no name column found on line 16 +[07:13:46] WARNING: no name column found on line 17 +[07:13:46] WARNING: no name column found on line 18 +[07:13:46] WARNING: no name column found on line 19 +[07:13:46] WARNING: no name column found on line 20 +[07:13:46] WARNING: no name column found on line 21 +[07:13:46] WARNING: no name column found on line 22 +[07:13:46] WARNING: no name column found on line 23 +[07:13:46] WARNING: no name column found on line 24 +[07:13:46] WARNING: no name column found on line 25 +[07:13:46] WARNING: no name column found on line 26 +[07:13:46] WARNING: no name column found on line 27 +[07:13:46] WARNING: no name column found on line 28 +[07:13:46] WARNING: no name column found on line 29 +[07:13:46] WARNING: no name column found on line 30 +[07:13:46] WARNING: no name column found on line 31 +[07:13:46] WARNING: no name column found on line 32 +[07:13:46] WARNING: no name column found on line 33 +[07:13:46] WARNING: no name column found on line 34 +[07:13:46] WARNING: no name column found on line 35 +[07:13:46] WARNING: no name column found on line 36 +[07:13:46] WARNING: no name column found on line 37 +[07:13:46] WARNING: no name column found on line 38 +[07:13:46] WARNING: no name column found on line 39 +[07:13:46] WARNING: no name column found on line 40 +[07:13:46] WARNING: no name column found on line 41 +[07:13:46] WARNING: no name column found on line 42 +[07:13:46] WARNING: no name column found on line 43 +[07:13:46] WARNING: no name column found on line 44 +[07:13:46] WARNING: no name column found on line 45 +[07:13:46] WARNING: no name column found on line 46 +[07:13:46] WARNING: no name column found on line 47 +[07:13:46] WARNING: no name column found on line 48 +[07:13:46] WARNING: no name column found on line 49 +[07:13:46] WARNING: no name column found on line 50 +[07:13:46] WARNING: no name column found on line 51 +[07:13:46] WARNING: no name column found on line 52 +[07:13:46] WARNING: no name column found on line 53 +[07:13:46] WARNING: no name column found on line 54 +[07:13:46] WARNING: no name column found on line 55 +[07:13:46] WARNING: no name column found on line 56 +[07:13:46] WARNING: no name column found on line 57 +[07:13:46] WARNING: no name column found on line 58 +[07:13:46] WARNING: no name column found on line 59 +[07:13:46] WARNING: no name column found on line 60 +[07:13:46] WARNING: no name column found on line 61 +[07:13:46] WARNING: no name column found on line 62 +[07:13:46] WARNING: no name column found on line 63 +[07:13:46] WARNING: no name column found on line 64 +[07:13:46] WARNING: no name column found on line 65 +[07:13:46] WARNING: no name column found on line 66 +[07:13:46] WARNING: no name column found on line 67 +[07:13:46] WARNING: no name column found on line 68 +[07:13:46] WARNING: no name column found on line 69 +[07:13:46] WARNING: no name column found on line 70 +[07:13:46] WARNING: no name column found on line 71 +[07:13:46] WARNING: no name column found on line 72 +[07:13:46] WARNING: no name column found on line 73 +[07:13:46] WARNING: no name column found on line 74 +[07:13:46] WARNING: no name column found on line 75 +[07:13:46] WARNING: no name column found on line 76 +[07:13:46] WARNING: no name column found on line 77 +[07:13:46] WARNING: no name column found on line 78 +[07:13:46] WARNING: no name column found on line 79 +[07:13:46] WARNING: no name column found on line 80 +[07:13:46] WARNING: no name column found on line 81 +[07:13:46] WARNING: no name column found on line 82 +[07:13:46] WARNING: no name column found on line 83 +[07:13:46] WARNING: no name column found on line 84 +[07:13:46] WARNING: no name column found on line 85 +[07:13:46] WARNING: no name column found on line 86 +[07:13:46] WARNING: no name column found on line 87 +[07:13:46] WARNING: no name column found on line 88 +[07:13:46] WARNING: no name column found on line 89 +[07:13:46] WARNING: no name column found on line 90 +[07:13:46] WARNING: no name column found on line 91 +[07:13:46] WARNING: no name column found on line 92 +[07:13:46] WARNING: no name column found on line 93 +[07:13:46] WARNING: no name column found on line 94 +[07:13:46] WARNING: no name column found on line 95 +[07:13:46] WARNING: no name column found on line 96 +[07:13:46] WARNING: no name column found on line 97 +[07:13:46] WARNING: no name column found on line 98 +[07:13:46] WARNING: no name column found on line 99 +[07:13:46] WARNING: no name column found on line 100 +[07:13:46] WARNING: no name column found on line 101 +[07:13:46] WARNING: no name column found on line 102 +[07:13:46] WARNING: no name column found on line 103 +[07:13:46] WARNING: no name column found on line 104 +[07:13:46] WARNING: no name column found on line 105 +[07:13:46] WARNING: no name column found on line 106 +[07:13:46] WARNING: no name column found on line 107 +[07:13:46] WARNING: no name column found on line 108 +[07:13:46] WARNING: no name column found on line 109 +[07:13:46] WARNING: no name column found on line 110 +[07:13:46] WARNING: no name column found on line 111 +[07:13:46] WARNING: no name column found on line 112 +[07:13:46] WARNING: no name column found on line 113 +[07:13:46] WARNING: no name column found on line 114 +[07:13:46] WARNING: no name column found on line 115 +[07:13:46] WARNING: no name column found on line 116 +[07:13:46] WARNING: no name column found on line 117 +[07:13:46] WARNING: no name column found on line 118 +[07:13:46] WARNING: no name column found on line 119 +[07:13:46] WARNING: no name column found on line 120 +[07:13:46] WARNING: no name column found on line 121 +[07:13:46] WARNING: no name column found on line 122 +[07:13:46] WARNING: no name column found on line 123 +[07:13:46] WARNING: no name column found on line 124 +[07:13:46] WARNING: no name column found on line 125 +[07:13:46] WARNING: no name column found on line 126 +[07:13:46] WARNING: no name column found on line 127 +[07:13:46] WARNING: no name column found on line 128 +[07:13:46] WARNING: no name column found on line 129 +[07:13:46] WARNING: no name column found on line 130 +[07:13:46] WARNING: no name column found on line 131 +[07:13:46] WARNING: no name column found on line 132 +[07:13:46] WARNING: no name column found on line 133 +[07:13:46] WARNING: no name column found on line 134 +[07:13:46] WARNING: no name column found on line 135 +[07:13:46] WARNING: no name column found on line 136 +[07:13:46] WARNING: no name column found on line 137 +[07:13:46] WARNING: no name column found on line 138 +[07:13:46] WARNING: no name column found on line 139 +[07:13:46] WARNING: no name column found on line 140 +[07:13:46] WARNING: no name column found on line 141 +[07:13:46] WARNING: no name column found on line 142 +[07:13:46] WARNING: no name column found on line 143 +[07:13:46] WARNING: no name column found on line 144 +[07:13:46] WARNING: no name column found on line 145 +[07:13:46] WARNING: no name column found on line 146 +[07:13:46] WARNING: no name column found on line 147 +[07:13:46] WARNING: no name column found on line 148 +[07:13:46] WARNING: no name column found on line 149 +[07:13:46] WARNING: no name column found on line 150 +[07:13:46] WARNING: no name column found on line 151 +[07:13:46] WARNING: no name column found on line 152 +[07:13:46] WARNING: no name column found on line 153 +[07:13:46] WARNING: no name column found on line 154 +[07:13:46] WARNING: no name column found on line 155 +[07:13:46] WARNING: no name column found on line 156 +[07:13:46] WARNING: no name column found on line 157 +[07:13:46] WARNING: no name column found on line 158 +[07:13:46] WARNING: no name column found on line 159 +[07:13:46] WARNING: no name column found on line 160 +[07:13:46] WARNING: no name column found on line 161 +[07:13:46] WARNING: no name column found on line 162 +[07:13:46] WARNING: no name column found on line 163 +[07:13:46] WARNING: no name column found on line 164 +[07:13:46] WARNING: no name column found on line 165 +[07:13:46] WARNING: no name column found on line 166 +[07:13:46] WARNING: no name column found on line 167 +[07:13:46] WARNING: no name column found on line 168 +[07:13:46] WARNING: no name column found on line 169 +[07:13:46] WARNING: no name column found on line 170 +[07:13:46] WARNING: no name column found on line 171 +[07:13:46] WARNING: no name column found on line 172 +[07:13:46] WARNING: no name column found on line 173 +[07:13:46] WARNING: no name column found on line 174 +[07:13:46] WARNING: no name column found on line 175 +[07:13:46] WARNING: no name column found on line 176 +[07:13:46] WARNING: no name column found on line 177 +[07:13:46] WARNING: no name column found on line 178 +[07:13:46] WARNING: no name column found on line 179 +[07:13:46] WARNING: no name column found on line 180 +[07:13:46] WARNING: no name column found on line 181 +[07:13:46] WARNING: no name column found on line 182 +[07:13:46] WARNING: no name column found on line 183 +[07:13:46] WARNING: no name column found on line 184 +[07:13:46] WARNING: no name column found on line 185 +[07:13:46] WARNING: no name column found on line 186 +[07:13:46] WARNING: no name column found on line 187 +[07:13:46] WARNING: no name column found on line 188 +[07:13:46] WARNING: no name column found on line 189 +[07:13:46] WARNING: no name column found on line 190 +[07:13:46] WARNING: no name column found on line 191 +[07:13:46] WARNING: no name column found on line 192 +[07:13:46] WARNING: no name column found on line 193 +[07:13:46] WARNING: no name column found on line 194 +[07:13:46] WARNING: no name column found on line 195 +[07:13:46] WARNING: no name column found on line 196 +[07:13:46] WARNING: no name column found on line 197 +[07:13:46] WARNING: no name column found on line 198 +[07:13:46] WARNING: no name column found on line 199 +[07:13:46] WARNING: no name column found on line 200 +[07:13:46] WARNING: no name column found on line 201 +[07:13:46] WARNING: no name column found on line 202 +[07:13:46] WARNING: no name column found on line 203 +[07:13:46] WARNING: no name column found on line 204 +[07:13:46] WARNING: no name column found on line 205 +[07:13:46] WARNING: no name column found on line 206 +[07:13:46] WARNING: no name column found on line 207 +[07:13:46] WARNING: no name column found on line 208 +[07:13:46] WARNING: no name column found on line 209 +[07:13:46] WARNING: no name column found on line 210 +[07:13:46] WARNING: no name column found on line 211 +[07:13:46] WARNING: no name column found on line 212 +[07:13:46] WARNING: no name column found on line 213 +[07:13:46] WARNING: no name column found on line 214 +[07:13:46] WARNING: no name column found on line 215 +[07:13:46] WARNING: no name column found on line 216 ...... ---------------------------------------------------------------------- -Ran 10 tests in 0.352s +Ran 10 tests in 0.289s OK .................. ---------------------------------------------------------------------- -Ran 18 tests in 3.409s +Ran 18 tests in 1.653s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.207s +Ran 3 tests in 0.190s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.158s +Ran 8 tests in 0.062s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.070s +Ran 2 tests in 0.050s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.053s +Ran 2 tests in 0.035s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.314s +Ran 1 test in 0.182s OK ........ @@ -32600,12 +32644,12 @@ OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.015s +Ran 3 tests in 0.011s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.004s +Ran 3 tests in 0.003s OK ...E @@ -32627,28 +32671,28 @@ RuntimeError: Incomplete pickle support (__getstate_manages_dict__ not set) ---------------------------------------------------------------------- -Ran 4 tests in 0.022s +Ran 4 tests in 0.013s FAILED (errors=1) !!! TEST FAILURE: python UnitTestFeatMapUtils.py {} ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.126s +Ran 7 tests in 0.032s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.052s +Ran 4 tests in 0.033s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 12.180s +Ran 4 tests in 5.645s OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.203s +Ran 10 tests in 0.099s OK . @@ -32658,7 +32702,7 @@ OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.035s +Ran 10 tests in 0.009s OK ....E @@ -32677,15 +32721,15 @@ TypeError: Random.shuffle() got an unexpected keyword argument 'random' ---------------------------------------------------------------------- -Ran 5 tests in 0.216s +Ran 5 tests in 0.090s FAILED (errors=1) !!! TEST FAILURE: python UnitTestGobbi.py {} -................[20:31:12] Molecule does not have explicit Hs. Consider calling AddHs() -[20:31:12] Molecule does not have explicit Hs. Consider calling AddHs() +................[07:14:20] Molecule does not have explicit Hs. Consider calling AddHs() +[07:14:20] Molecule does not have explicit Hs. Consider calling AddHs() ..... ---------------------------------------------------------------------- -Ran 21 tests in 22.772s +Ran 21 tests in 10.935s OK mol_197 @@ -32699,7 +32743,7 @@ Ran 1 test in 0.001s OK -...[20:31:15] +...[07:14:21] **** Pre-condition Violation @@ -32710,65 +32754,65 @@ . ---------------------------------------------------------------------- -Ran 4 tests in 0.127s +Ran 4 tests in 0.050s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 32.760s +Ran 2 tests in 16.404s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.285s +Ran 2 tests in 0.199s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.039s +Ran 3 tests in 0.024s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.074s +Ran 4 tests in 0.050s OK -.....[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors -[20:31:58] WARNING: not removing hydrogen atom without neighbors +.....[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors +[07:14:43] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- -Ran 10 tests in 1.081s +Ran 10 tests in 0.785s OK -ssssss[20:32:02] No suitable metadata found. -.[20:32:02] No suitable metadata found. +ssssss[07:14:44] No suitable metadata found. +.[07:14:44] No suitable metadata found. ......s/build/rdkit-202209.3/obj-aarch64-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 2.496s +Ran 19 tests in 0.918s OK (skipped=7) sss. ---------------------------------------------------------------------- -Ran 4 tests in 3.690s +Ran 4 tests in 1.761s OK (skipped=3) sss @@ -32778,33 +32822,33 @@ OK (skipped=3) .......... ---------------------------------------------------------------------- -Ran 10 tests in 2.599s +Ran 10 tests in 1.259s OK -..[20:32:17] SMARTS Parse Error: syntax error while parsing: boromicacid -[20:32:17] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -[20:32:17] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -[20:32:17] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -[20:32:17] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -[20:32:17] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -[20:32:17] reaction has no reactants -[20:32:17] reaction has no products -[20:32:17] initialization failed -[20:32:17] reaction has no reactants -[20:32:17] reaction has no products +..[07:14:52] SMARTS Parse Error: syntax error while parsing: boromicacid +[07:14:52] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +[07:14:52] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +[07:14:52] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +[07:14:52] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +[07:14:52] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +[07:14:52] reaction has no reactants +[07:14:52] reaction has no products +[07:14:52] initialization failed +[07:14:52] reaction has no reactants +[07:14:52] reaction has no products . ---------------------------------------------------------------------- -Ran 3 tests in 0.074s +Ran 3 tests in 0.066s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.035s +Ran 4 tests in 0.022s OK .................... ---------------------------------------------------------------------- -Ran 20 tests in 0.543s +Ran 20 tests in 0.219s OK !!! TEST FAILURE: python UnitTestGraphDescriptors_2.py {} @@ -32814,14 +32858,10 @@ !!! TEST FAILURE: python test_list.py {'dir': 'FeatMaps'} !!! TEST FAILURE: python test_list.py {'dir': 'Pharm2D'} -5: [20:35:33] Finished: testMultipleTimes() -5: [20:35:33] -5: ----------------------------------------- -208/208 Test #5: testConcurrentQueue .................... Passed 1127.84 sec 97% tests passed, 6 tests failed out of 208 -Total Test time (real) = 1127.90 sec +Total Test time (real) = 338.86 sec The following tests FAILED: 22 - pyAlignment (Failed) @@ -35505,27 +35545,27 @@ 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 librdkit-dev: 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: Depends field of package rdkit-data: 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 librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package rdkit-data: 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 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: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package python3-rdkit: substitution variable ${python3:Versions} used, but is not defined -dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package rdkit-doc: 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 librdkit-dev: 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 postgresql-15-rdkit: substitution variable ${postgresql:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-15-rdkit: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package librdkit1: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: 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' in '../python3-rdkit_202209.3-1_arm64.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202209.3-1_all.deb'. dpkg-deb: building package 'librdkit1' in '../librdkit1_202209.3-1_arm64.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202209.3-1_all.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202209.3-1_arm64.deb'. dpkg-deb: building package 'postgresql-15-rdkit-dbgsym' in '../postgresql-15-rdkit-dbgsym_202209.3-1_arm64.deb'. dpkg-deb: building package 'postgresql-15-rdkit' in '../postgresql-15-rdkit_202209.3-1_arm64.deb'. @@ -35539,12 +35579,14 @@ 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/14287/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/14287/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/12876 and its subdirectories -I: Current time: Mon Apr 17 20:43:19 -12 2023 -I: pbuilder-time-stamp: 1681807399 +I: removing directory /srv/workspace/pbuilder/14287 and its subdirectories +I: Current time: Tue May 21 07:19:12 +14 2024 +I: pbuilder-time-stamp: 1716225552