Diff of the two buildlogs: -- --- b1/build.log 2024-05-10 15:21:59.367972679 +0000 +++ b2/build.log 2024-05-10 16:18:03.368762030 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 10 02:56:15 -12 2024 -I: pbuilder-time-stamp: 1715352975 +I: Current time: Fri Jun 13 11:45:44 +14 2025 +I: pbuilder-time-stamp: 1749764744 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying pg16 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3420888/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2570913/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Jun 12 21:45 /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/2570913/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2570913/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + 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=12 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='88a8daa2da164dd4b435a8648d0ba364' - 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='3420888' - PS1='# ' - PS2='> ' + INVOCATION_ID=756e19cb562642d58ead189c4a6353e8 + 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=2570913 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.ShPTGvri/pbuilderrc_1JBZ --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ShPTGvri/b1 --logfile b1/build.log rdkit_202309.3-4~exp1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.ShPTGvri/pbuilderrc_JJ2d --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ShPTGvri/b2 --logfile b2/build.log rdkit_202309.3-4~exp1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 7 07:33 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3420888/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 13:58 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2570913/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -532,7 +564,7 @@ Get: 340 http://deb.debian.org/debian unstable/main arm64 texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 341 http://deb.debian.org/debian unstable/main arm64 texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 342 http://deb.debian.org/debian unstable/main arm64 texlive-latex-extra all 2023.20240207-1 [19.7 MB] -Fetched 378 MB in 2s (219 MB/s) +Fetched 378 MB in 3s (120 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 ... 19744 files and directories currently installed.) @@ -1628,8 +1660,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri May 10 14:57:10 UTC 2024. -Universal Time is now: Fri May 10 14:57:10 UTC 2024. +Local time is now: Thu Jun 12 21:47:11 UTC 2025. +Universal Time is now: Thu Jun 12 21:47:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:arm64 (1.83.0-2.1+b1) ... @@ -1779,11 +1811,6 @@ Setting up pandoc (3.1.3+ds-3) ... Setting up libfreetype6:arm64 (2.13.2+dfsg-1+b4) ... Setting up ssl-cert (1.1.2) ... -hostname: Name or service not known -make-ssl-cert: Could not get FQDN, using 'codethink04-arm64'. -make-ssl-cert: You may want to fix your /etc/hosts and/or DNS setup and run -make-ssl-cert: 'make-ssl-cert generate-default-snakeoil --force-overwrite' -make-ssl-cert: again. Setting up libboost-date-time1.83-dev:arm64 (1.83.0-2.1+b1) ... Setting up x11proto-core-dev (2024.1-1) ... Setting up shared-mime-info (2.4-4) ... @@ -1995,7 +2022,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202309.3/ && 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_202309.3-4~exp1_source.changes +I: user script /srv/workspace/pbuilder/2570913/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/2570913/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202309.3/ && 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_202309.3-4~exp1_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202309.3-4~exp1 dpkg-buildpackage: info: source distribution experimental @@ -2179,94 +2210,94 @@ cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/INCHI-API /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake "--color=" make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend -make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh/hcdriver.c -[ 2%] Linking C shared library ../../../../lib/libRDKithc.so -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 -/usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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-c /build/reproducible-path/rdkit-202309.3/External/GA/util/Util.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2023.09.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 2%] Built target hc -[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -MF CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o.d -o CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/catch_logs.cpp +[ 3%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/DistPicker.cpp +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseBitVect.cpp +[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/ExplicitBitVect.cpp [ 4%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so 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CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/ExplicitBitVect.cpp cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 4%] Built target EigenSolvers +[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Utils.cpp +[ 4%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogParams.cpp [ 4%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogEntry.cpp -[ 4%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/MaxMinPicker.cpp [ 4%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -2431,19 +2462,26 @@ cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 4%] Built target Catalogs -[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Utils.cpp +[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/base64.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 4%] Built target logTestsCatch -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp -[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.cpp +[ 4%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.cpp +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteValueVect.cpp [ 5%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd 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/usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/FPBReader.cpp +[ 5%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-2453,39 +2491,32 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 5%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/RDBoost/Wrap && /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 -DrdBase_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o -MF CMakeFiles/rdBase.dir/RDBase.cpp.o.d -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap/RDBase.cpp +[ 5%] Built target testMatrices make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd 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-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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh/Clustering.cpp -[ 6%] Linking CXX executable testMatrices -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/MultiFPBReader.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 6%] Built target dictTestsCatch -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteValueVect.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 6%] Built target testMatrices -[ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/FPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/FPBReader.cpp [ 6%] Linking CXX executable testQuery cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -g 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -MF CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o.d -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/MultiFPBReader.cpp [ 6%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp +[ 12%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/build/reproducible-path/rdkit-202309.3/Code/Geometry/testGrid.cpp +[ 15%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap && /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 -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp +[ 15%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 +[ 15%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here @@ -2622,6 +2760,7 @@ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:90:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 90 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkTversky(const T&, boost::python::list, double, double, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:211:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here @@ -2637,6 +2776,7 @@ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:14: warning: possibly dangling reference to a temporary [-Wdangling-reference] 77 | const T &siv2 = python::extract(sivs[i])(); | ^~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:77:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 77 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ @@ -2685,6 +2825,9 @@ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 15%] Built target Alignment +make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = long unsigned int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:222:29: required from here @@ -2712,153 +2855,28 @@ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 9%] Linking CXX executable pickersTestsCatch -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKithc.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 9%] Built target pickersTestsCatch -[ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.cpp -[ 9%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 9%] Built target InfoTheory -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 9%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap && /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 -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp -[ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /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 -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp -[ 9%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -[ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/rdGeometry.cpp [ 15%] Linking CXX executable testGrid cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -2872,89 +2890,117 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 15%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o cd 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../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 15%] Linking CXX executable testDataStructs +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryAtom.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 15%] Built target rdSimDivPickers +[ 15%] Built target geometryTestsCatch make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp -[ 18%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +[ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 18%] Built target ChemicalFeatures +[ 17%] Built target ChemicalFeatures make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[4]: Entering directory 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/usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 19%] Built target cDataStructs +[ 19%] Built target rdBase [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp -[ 19%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /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 -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/UniformGrid3D.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp:72:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] 72 | if (res < 0) { @@ -3011,8 +3044,13 @@ cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Matrices.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.cpp +[ 19%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 20%] Built target cDataStructs [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o @@ -3027,21 +3065,14 @@ cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.cpp -[ 20%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap && /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 -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/rdGeometry.cpp -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindStereo.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o +[ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindStereo.cpp cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/NontetrahedralStereo.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/WedgeBonds.cpp -[ 21%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 21%] Built target rdGeometry [ 21%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2023.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -3049,1084 +3080,915 @@ make[4]: Leaving directory 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[4]: Leaving directory 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/MolTransforms.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build make[4]: Entering 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o +[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o +make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp +[ 21%] Building CXX object 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f 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CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -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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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/smiles.tab.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd 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-fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so +cd 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Trajectory.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 23%] Built target GenericGroups -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend +[ 22%] Built target PartialCharges +make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. 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-Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2023.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 23%] Built target MolTransforms +[ 23%] Building CXX object 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Queries.cpp +[ 23%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/sln.tab.cpp -[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/BondStretch.cpp -[ 27%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Nonbonded.cpp -[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -MF CMakeFiles/graphmolIterTest.dir/itertest.cpp.o.d -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/itertest.cpp +[ 30%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -[ 28%] Built target rdqueries -[ 29%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/lex.yysln.cpp +[ 30%] Built target rdqueries +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make 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CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp -[ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 30%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/memtest1.cpp +[ 30%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -[ 29%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -[ 29%] Built target rdMolTransforms -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 29%] Built target ShapeHelpers -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend +[ 30%] Built target rdMolTransforms +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake "--color=" -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionAngle.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp -[ 29%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.cpp -[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && 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Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 31%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202309.3/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 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2023.09.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleBend.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 31%] Built target SLNParse -make -f 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +[ 30%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -[ 31%] Built target MolInterchange -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend +[ 30%] Built target MolInterchange +make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.cpp -[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleBend.cpp -[ 31%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.cpp -[ 31%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -cd 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object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Nonbonded.cpp -[ 31%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E 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Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleConstraint.cpp -[ 32%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so -cd /build/reproducible-path/rdkit-202309.3/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 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/usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 32%] Built target SubstructMatch -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION 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ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': -/build/reproducible-path/rdkit-202309.3/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) { - | ^ -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.cpp -[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp +[ 30%] Built target SLNParse +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 32%] Built target rdSLNParse -[ 32%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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 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Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp -[ 34%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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-D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 35%] Built target rdMolInterchange -[ 35%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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 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&& /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" +[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 35%] Built target ForceField -[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202309.3/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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/BondStretch.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 30%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/test2.cpp +[ 30%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 35%] Built target rdCIPLabeler -[ 35%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so +[ 30%] Built target graphmolcpTest +make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 35%] Built target SmilesParse -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend +make -f Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/catch_tests.cpp +[ 31%] Linking CXX executable graphmolMemTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make 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Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so make[4]: Leaving directory 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 46%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o +[ 42%] Building CXX object Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap && /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 -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::UFFConfsHelper(ROMol&, int, int, double, bool)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: warning: redundant move in return statement [-Wredundant-move] - 49 | return std::move(pyres); - | ~~~~~~~~~^~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: note: remove 'std::move' call -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::MMFFConfsHelper(ROMol&, int, int, std::string, double, bool)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: warning: redundant move in return statement [-Wredundant-move] - 66 | return std::move(pyres); - | ~~~~~~~~~^~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: note: remove 'std::move' call -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::FFConfsHelper(ROMol&, ForceFields::PyForceField&, int, int)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: warning: redundant move in return statement [-Wredundant-move] - 86 | return std::move(pyres); - | ~~~~~~~~~^~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: note: remove 'std::move' call -[ 46%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +[ 42%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202309.3/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 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../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 46%] Built target DistGeometry -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend +[ 42%] Built target rdCoordGen +make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 48%] Built target rdReducedGraphs -[ 48%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +[ 42%] Built target testSLNParse +[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp -[ 48%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E 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Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.cpp +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.cpp +[ 42%] Linking CXX executable testReducedGraphs +cd /build/reproducible-path/rdkit-202309.3/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 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 48%] Built target rdForceFieldHelpers -[ 48%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp -[ 49%] Linking CXX executable testDistGeom -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 42%] Built target testReducedGraphs +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd 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../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 43%] Built target rdReducedGraphs +[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp +[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 49%] Built target testDistGeom -[ 49%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +[ 43%] Built target rdCIPLabeler +[ 43%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +[ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /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 -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp -[ 49%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +[ 43%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp +[ 43%] Linking CXX shared library ../../lib/libRDKitForceField.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 49%] Built target O3AAlign -[ 49%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp -[ 49%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 43%] Built target ForceField +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 49%] Built target DistGeom -[ 49%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o +cd 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp +[ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap && /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 -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp -[ 49%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp -[ 49%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Templates.cpp -[ 49%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 49%] Built target rdAbbreviations -[ 49%] Building CXX object 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp -[ 49%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp +[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 49%] Built target rdMolChemicalFeatures -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 49%] Built target FilterCatalog -make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap 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Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp -[ 50%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 50%] Built target DistGeomHelpers -[ 51%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +[ 45%] Built target rdMolChemicalFeatures +[ 45%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp +[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 46%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 51%] Built target Fingerprints +[ 46%] Built target Fingerprints make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/DependInfo.cmake "--color=" @@ -4139,10 +4001,38 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 51%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -[ 51%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +[ 46%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap && /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 -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': +/build/reproducible-path/rdkit-202309.3/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); + | ^ +[ 47%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 47%] Built target Depictor +make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap 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Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp +[ 47%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp +[ 47%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitPathsHelper(const RDKit::AdditionalOutput&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: warning: redundant move in return statement [-Wredundant-move] 452 | return std::move(res); @@ -4153,37 +4043,182 @@ 467 | return std::move(res); | ~~~~~~~~~^~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: note: remove 'std::move' call -[ 51%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +[ 47%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 47%] Built target FilterCatalog +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp +[ 47%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202309.3/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 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 47%] Built target ForceFieldHelpers +make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/DistGeometry.dir/DependInfo.cmake "--color=" +make[4]: Entering directory 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CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +[ 48%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp +[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistViolationContrib.cpp +[ 49%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralViolationContrib.cpp +[ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 51%] Built target rdDepictor -[ 51%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so +[ 49%] Built target rdMHFPFingerprint +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 49%] Built target rdDepictor +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::UFFConfsHelper(ROMol&, int, int, double, bool)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: warning: redundant move in return statement [-Wredundant-move] + 49 | return std::move(pyres); + | ~~~~~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: note: remove 'std::move' call +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::MMFFConfsHelper(ROMol&, int, int, std::string, double, bool)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: warning: redundant move in return statement [-Wredundant-move] + 66 | return std::move(pyres); + | ~~~~~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:66:19: note: remove 'std::move' call +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::FFConfsHelper(ROMol&, ForceFields::PyForceField&, int, int)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: warning: redundant move in return statement [-Wredundant-move] + 86 | return std::move(pyres); + | ~~~~~~~~~^~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: note: remove 'std::move' call +[ 49%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 49%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 49%] Built target ChemTransforms make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 51%] Built target ChemTransforms make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" +[ 49%] Built target DistGeometry +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDWriter.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/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 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTWriter.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 52%] Built target DistGeomHelpers [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/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 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TplFileParser.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TplFileWriter.cpp -[ 52%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o -MF CMakeFiles/FileParsers.dir/PDBParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PDBParser.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o @@ -4236,19 +4267,19 @@ cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceWriters.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SVGParser.cpp -[ 54%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PNGParser.cpp -[ 54%] Built target rdfiltercatalog [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp +[ 54%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 54%] Built target rdfiltercatalog [ 54%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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/MaeWriter.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/libRDKitChemTransforms.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -4257,100 +4288,100 @@ [ 54%] Built target FileParsers make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202309.3/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 -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/UFF /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/MMFF /build/reproducible-path/rdkit-202309.3/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[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/testMMFFForceField.cpp -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/test1.cpp make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp [ 54%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o cd 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testSGroup.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/resMolSupplierTest.cpp [ 55%] Linking CXX executable molBundleTest cd 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../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4377,11 +4408,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o cd 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Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -MF CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o.d -o CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_organometallics.cpp -[ 55%] Linking CXX executable testCoordGen -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/aarch64-linux-gnu/libcoordgen.so 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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/libmaeparser.so +[ 55%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 55%] Built target testCoordGen +[ 55%] Built target graphmoltestPicklerGlobalSetting make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake "--color=" @@ -4390,37 +4421,37 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 55%] Building CXX object 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_sgroups.cpp -[ 55%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 56%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 55%] Built target graphmoltestPicklerGlobalSetting +[ 56%] Built target hanoiTest make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" +[ 56%] Linking CXX executable testUFFForceField +cd 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_adjustquery.cpp -[ 56%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 56%] Built target testUFFForceField +[ 57%] Built target testUFFForceField make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o +[ 57%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/chiralityTestsCatch.dir/catch_chirality.cpp.o -MF CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o.d -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_chirality.cpp -[ 57%] Linking CXX executable hanoiTest -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 57%] Linking CXX executable testCoordGen +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/aarch64-linux-gnu/libcoordgen.so 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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/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 57%] Built target hanoiTest +[ 57%] Built target testCoordGen make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" @@ -4432,19 +4463,19 @@ [ 57%] Linking CXX executable graphmolTest1 cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so +[ 58%] Linking CXX executable graphmolOrganometallicsCatch +cd 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../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 57%] Built target graphmolTest1 +[ 58%] Built target graphmolTest1 make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 57%] Building CXX object Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o +[ 58%] Building CXX object Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/pickleTestsCatch.dir/catch_pickles.cpp.o -MF CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o.d -o CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_pickles.cpp -[ 58%] Linking CXX executable graphmolOrganometallicsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -o graphmolOrganometallicsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 58%] Built target graphmolOrganometallicsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend @@ -4536,11 +4567,8 @@ [ 58%] Linking CXX executable pickleTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -[ 58%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 58%] Built target graphmoltestChirality +[ 58%] Built target pickleTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" @@ -4549,8 +4577,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 58%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/test1.cpp +[ 58%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 58%] Built target pickleTestsCatch +[ 58%] Built target graphmoltestChirality make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" @@ -4572,6 +4603,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 59%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testGeneralFileReader.cpp +[ 59%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp [ 59%] Linking CXX executable cxsmilesTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4585,12 +4618,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp -[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 70 | const std::vector &atom_props) { - | ^ [ 60%] Linking CXX executable testDepictor cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4604,11 +4631,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMolWriter.cpp -[ 60%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 70 | const std::vector &atom_props) { + | ^ +[ 60%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 60%] Built target testGeneralFileReader +[ 60%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" @@ -4617,24 +4648,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testTpls.cpp -[ 60%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so +[ 60%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 60%] Built target testMultithreadedMolSupplier +[ 60%] Built target testGeneralFileReader make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" -[ 60%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMol2ToMol.cpp +[ 61%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 61%] Built target graphmolTestsCatch +[ 61%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" @@ -4643,11 +4674,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testSequence.cpp -[ 61%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 61%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 61%] Built target testSequence +[ 61%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" @@ -4656,11 +4687,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp +[ 61%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so [ 61%] Linking CXX executable testTplParser cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 61%] Built target testTplParser +[ 61%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -4669,11 +4703,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 61%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 61%] Built target testMol2ToMol +[ 61%] Built target testTplParser make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake "--color=" @@ -4682,37 +4713,37 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testPropertyLists.cpp -[ 61%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 +[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.cpp [ 61%] Linking CXX executable testExtendedStereoParsing cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 61%] Built target testExtendedStereoParsing make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" -[ 61%] Built target smiTest1 -make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp +[ 61%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 61%] Built target testMolWriter +make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -[ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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 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directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 62%] Built target testMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend @@ -4723,52 +4754,52 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -[ 63%] Linking CXX executable chiralityTestsCatch -cd 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Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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"--color=" -[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection 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-ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 63%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 63%] Built target depictorCatch +[ 63%] Built target smiTestCatch make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" @@ -4790,11 +4821,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -[ 63%] Linking CXX executable testPropertyLists -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 63%] Linking CXX executable connectTheDotsTest +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 63%] Built target testPropertyLists +[ 63%] Built target connectTheDotsTest make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" @@ -4803,11 +4834,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/catch_tests.cpp -[ 63%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 63%] Linking CXX executable testPropertyLists +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 63%] Built target connectTheDotsTest +[ 63%] 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/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake "--color=" @@ -4819,6 +4850,9 @@ [ 63%] Linking CXX executable molfileStereoCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 63%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 63%] Built target molfileStereoCatchTest make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend @@ -4829,11 +4863,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/test1.cpp -[ 63%] Linking CXX executable cdxmlParserCatchTest -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 63%] Built target cdxmlParserCatchTest make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend @@ -4844,47 +4873,49 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 63%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /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 -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rdfragcatalog.cpp -[ 64%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /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 -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp -[ 64%] Linking CXX executable graphmolMolOpsTest +[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.cpp +[ 63%] Linking CXX executable graphmolMolOpsTest cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 64%] Built target graphmolMolOpsTest +[ 63%] Built target graphmolMolOpsTest make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/test1.cpp -[ 64%] Linking CXX executable substructTestCatch +[ 63%] Linking CXX executable substructTestCatch cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 64%] Built target substructTestCatch +[ 63%] Built target substructTestCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp -[ 64%] Linking CXX executable testGenericGroups +[ 63%] Linking CXX executable testGenericGroups cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 64%] Built target testGenericGroups +[ 63%] Built target testGenericGroups make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o +[ 63%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp +[ 64%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /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 -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp [ 64%] Linking CXX executable filterCatalogTest cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -4903,6 +4934,9 @@ [ 64%] Linking CXX executable testFragCatalog cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 64%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 64%] Built target testFragCatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend @@ -4913,9 +4947,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 64%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -MF CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o.d -o CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp -[ 64%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 64%] Built target testSubstructMatch make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend @@ -4954,26 +4985,26 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 65%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -[ 66%] Linking CXX executable chemTransformsTestCatch -cd 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 66%] Built target chemTransformsTestCatch +[ 66%] Built target fileParsersTest1 make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake "--color=" @@ -4984,11 +5015,11 @@ cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.cpp -[ 66%] Linking CXX executable fpGenTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 66%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 66%] Built target fpGenTestCatch +[ 66%] Built target testMolTransforms make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" @@ -4997,11 +5028,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -MF CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o.d -o CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp -[ 66%] Linking CXX executable testMolTransforms -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 66%] Linking CXX executable fpGenTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 66%] Built target testMolTransforms +[ 66%] Built target fpGenTestCatch make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" @@ -5010,24 +5041,32 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 66%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp -[ 67%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 66%] Linking CXX executable fpTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -o fpTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 67%] Built target testMMFFForceFieldHelpersMultiThread +[ 66%] Built target fpTestCatch make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make 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Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp +[ 67%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 67%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 +[ 67%] Linking CXX executable fileParsersCatchTest +cd 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../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 67%] Built target fpTestCatch +[ 67%] Built target testMMFFForceFieldHelpersMultiThread 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_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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../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so -[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /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 -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 67%] Built target testCrystalForceField +[ 67%] Built target testMMFFForceFieldHelpers make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake "--color=" @@ -5051,13 +5085,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp -[ 67%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR2D.cpp -[ 67%] Built target testMMFFForceFieldHelpers +[ 67%] Built target fileParsersCatchTest make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake "--color=" @@ -5066,11 +5095,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp -[ 67%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 67%] Linking CXX executable testCrystalForceField +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 67%] Built target testFingerprintGenerators +[ 67%] Built target testCrystalForceField make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake "--color=" @@ -5079,11 +5108,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 67%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/test1.cpp -[ 67%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 67%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp +[ 67%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.cpp -[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp -[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /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 -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp -[ 67%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF && 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../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so 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../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 68%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 67%] Built target testUFFForceFieldHelpers +[ 68%] Built target testFingerprints make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o +[ 68%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o cd 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.cpp -[ 67%] Built target testShapeHelpers +[ 68%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp +[ 68%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 68%] Built target molAlignCatchTest make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 67%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o +[ 68%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -MF CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/catch_tests.cpp -[ 68%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 68%] Linking CXX executable testMolCatalog +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 68%] Built target testFingerprints +[ 68%] Built target testMolCatalog make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/trajectoryTest.cpp -[ 68%] Linking CXX executable distGeomHelpersCatch -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/USRDescriptor.cpp +[ 68%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202309.3/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 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../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 68%] Built target distGeomHelpersCatch +[ 68%] Built target testUFFForceFieldHelpers make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake "--color=" @@ -5165,11 +5194,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/test1.cpp -[ 69%] Linking CXX executable testMolCatalog -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolCatalog.dir/test1.cpp.o -o testMolCatalog ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +[ 69%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 69%] Built target testMolCatalog +[ 69%] 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/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" @@ -5178,11 +5207,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -[ 69%] Linking CXX executable testFeatures -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures && 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../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 69%] Built target testFeatures +[ 69%] Built target distGeomHelpersCatch make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/DependInfo.cmake "--color=" @@ -5191,188 +5220,190 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 69%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AtomFeat.cpp [ 69%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -MF CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o.d -o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.cpp +[ 69%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2023.09.3 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -MF CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o.d -o CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA_UnitTest.cpp -[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalCluster.cpp +[ 72%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 +[ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalCluster.cpp -[ 71%] Linking CXX executable molInterchangeTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o +[ 72%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/CoulombMat.cpp [ 75%] Linking CXX shared library ../../../lib/libRDKitFMCS.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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.1.2023.09.3 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-ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 75%] 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/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS 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/usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 77%] Built target testCIPLabeler /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp: In function 'boost::python::api::object {anonymous}::degenerateSmartsQueryMolDictHelper(const RDKit::MCSResult&)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: warning: redundant move in return statement [-Wredundant-move] 646 | return std::move(res); @@ -5394,8 +5425,8 @@ make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' @@ -5403,128 +5434,130 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 77%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o [ 77%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -[ 77%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/mces_catch.cpp +[ 77%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -MF CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o.d -o CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -MF CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o.d -o CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/mces_catch.cpp +[ 77%] Building CXX object Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /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 -DrdRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp +[ 77%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl [ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 77%] Built target rdFMCS -[ 77%] Linking CXX executable testRascalCluster -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 77%] Built target testRascalCluster -[ 77%] Linking CXX executable testFMCS -cd 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:437:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 437 | python::list atomprops) { | ^ -[ 83%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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 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Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 84%] Built target testAUTOCORR3D +[ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/normalize.cpp In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:17, @@ -5738,6 +5764,16 @@ cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp [ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp +[ 84%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 84%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 84%] Built target testMolAlign +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 84%] Built target descriptorsTestCatch [ 84%] Linking CXX shared library ../../../lib/libRDKitMolHash.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -5746,23 +5782,18 @@ [ 84%] Built target MolHash make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/catch_tests.cpp -[ 84%] Linking CXX executable testMolAlign -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 84%] Built target testMolAlign make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 84%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/catch_tests.cpp [ 84%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap && /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 -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp [ 84%] Linking CXX executable testO3AAlign @@ -5782,102 +5813,104 @@ [ 84%] Built target rdMolHash [ 84%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl [ 84%] Linking CXX executable molHashCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 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.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so 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/usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 84%] Built target molHashCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1 ../../../lib/libRDKitChemReactions.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 84%] Built target ChemReactions make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/depend -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 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testReaction.cpp +[ 85%] Building CXX object 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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'/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 85%] Built target molHashCatchTest +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp [ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script 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directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdmolops.cpp In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:17, @@ -5889,10 +5922,6 @@ /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 86%] Built target rdMolDescriptors -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ChiralityOps.cpp [ 86%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -5907,6 +5936,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 86%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/deprotectTest.cpp +[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp [ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/PositionVariation.cpp [ 86%] Linking CXX executable testReactionFingerprints @@ -5922,71 +5953,71 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 86%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp -[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.cpp [ 86%] Linking CXX executable testEnumeration cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 86%] Built target testEnumeration +[ 86%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DSVG.cpp +[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.cpp [ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.cpp -[ 86%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -cd 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-Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp +[ 87%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[ 87%] Built target MarvinParser +make -f Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -MF CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o.d -o CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/testMrvToMol.cpp +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp [ 88%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 88%] Built target rdDeprotect -[ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -[ 88%] Building CXX object 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Charge.cpp -[ 88%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, @@ -5998,6 +6029,8 @@ | ^~~~~~~~~~~~~ [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp In file included from /usr/include/c++/13/algorithm:60: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, @@ -6051,124 +6073,80 @@ /usr/include/c++/13/bits/new_allocator.h:151:55: note: at offset [-9223372036854775808, -1] into destination object of size [4, 9223372036854775804] allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 89%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 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../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ChiralityOps.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o +cd 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp +[ 91%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o 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../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 91%] Built target MolDraw2D -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make 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/build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp -[ 92%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 92%] Built target testMolEnumerator -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +[ 91%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make 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/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +[ 91%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap && /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 -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, @@ -6196,8 +6174,41 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: note: '' declared here 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so 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object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Table.cpp +[ 93%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 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/usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 93%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /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 -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c 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+cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp -[ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 94%] Linking CXX executable moldraw2DRxnTest1 +cd 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -6302,11 +6337,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testNormalize.cpp -[ 96%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libcairo.so /usr/lib/aarch64-linux-gnu/libfreetype.so +[ 96%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 96%] Built target moldraw2DTest1 +[ 96%] Built target TautomerQuery make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" @@ -6315,35 +6351,25 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testValidate.cpp -[ 96%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Mol.cpp +[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Conformer.cpp +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Conformer.cpp -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD 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/usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 96%] Built target molNormalizeTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu 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cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so 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../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 96%] Built target molValidateTest make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend @@ -6365,34 +6401,37 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/test2.cpp -[ 97%] Linking CXX executable molStandardizeTest -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize && 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/catch_tests.cpp +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 97%] Built target molChargeTest make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend make[4]: Entering directory 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/EditableMol.cpp -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MonomerInfo.cpp -[ 97%] Linking CXX executable molStandardizeSmallTest -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 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/usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl [ 97%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared 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/usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[ 97%] Linking CXX executable molStandardizeSmallTest +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so 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molStandardizeSmallTest make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake "--color=" @@ -6434,42 +6467,40 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 97%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp [ 98%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so cd /build/reproducible-path/rdkit-202309.3/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 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../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -6483,25 +6514,25 @@ make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o +[ 98%] Linking CXX executable molTautomerTest cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp -[ 99%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -[ 99%] Linking CXX executable molTautomerTest cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 99%] Built target tautomerQueryTestCatch +[ 98%] Built target molTautomerTest make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 99%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o +[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[ 99%] Built target molTautomerTest +[ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Chirality.cpp +[ 99%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" @@ -6510,8 +6541,10 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [ 99%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap && /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 -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -[ 99%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap && /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 -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp [100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp -[100%] Building CXX object 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp +[100%] Linking CXX executable testScaffoldNetwork +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[100%] Built target testScaffoldNetwork +[100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o +cd 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target GeneralizedSubstruct @@ -6554,15 +6594,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp -[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp -[100%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp +[100%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[100%] Built target testScaffoldNetwork +[100%] Built target rdchem make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" @@ -6571,15 +6609,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp -[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -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_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp -[100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd 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../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl [100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /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 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-c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[100%] Built target rdScaffoldNetwork make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" @@ -6588,15 +6619,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /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 -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp +[100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl [100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /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 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/usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[100%] Built target rdScaffoldNetwork [100%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap && /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 -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[100%] Built target rdchem [100%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so cd 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CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -6604,8 +6635,8 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target RGroupDecomposition make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend @@ -6619,22 +6650,22 @@ make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make 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Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -[100%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o +[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp +[100%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /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 -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp [100%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -6645,6 +6676,16 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target generalizedSubstructCatch +[100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[100%] Built target rdMolStandardize +[100%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[100%] Built target testRGroupDecompInternals [100%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=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.1.2023.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl /usr/lib/aarch64-linux-gnu/libmaeparser.so @@ -6652,41 +6693,31 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/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]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /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 -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /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 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CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp -[100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -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.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[100%] Built target rdMolStandardize -[100%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[100%] Built target testRGroupDecompInternals +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /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 -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap && /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 -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp [100%] Linking CXX executable rgroupCatchTests cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -6697,16 +6728,16 @@ /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitga.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' [100%] Built target rdRGroupDecomposition -[100%] Linking CXX executable substructLibraryTest -cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' -[100%] Built target substructLibraryTest [100%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl +[100%] Linking CXX executable substructLibraryTest +cd /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl [100%] Built target substructLibraryCatchTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu' +[100%] Built target substructLibraryTest [100%] Linking CXX executable testRGroupDecomp cd /build/reproducible-path/rdkit-202309.3/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/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -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.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_serialization.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_serialization.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so -ldl @@ -11163,13 +11194,13 @@ 1: 2 5 1 0 1: M END 1: -3: [03:17:28] Testing Github940: property dictionaries leaking memory -3: [03:17:28] done +3: [12:24:52] Testing Github940: property dictionaries leaking memory +3: [12:24:52] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect -3: static boost any:0.046863 s +3: static boost any:0.053192 s 4: -- running tests -- 4: min: -2147483648 -2147483648 4: min: 0 0 @@ -11182,28 +11213,28 @@ 4: == unsigned int 4: == bool 4: == std::string -5: [03:17:28] +5: [12:24:52] 5: ----------------------------------------- -5: [03:17:28] Finished: testPushAndPop() -5: [03:17:28] +5: [12:24:52] Finished: testPushAndPop() +5: [12:24:52] 5: ----------------------------------------- -5: [03:17:28] +5: [12:24:52] 5: ----------------------------------------- -6: Randomness seeded to: 1745921784 +6: Randomness seeded to: 981440702 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: -7: [03:17:28] should not be silent -7: [03:17:28] should not be silent -7: Randomness seeded to: 2603848127 -7: [03:17:28] should not be silent -7: [03:17:28] should not be silent -7: [03:17:28] should not be silent -7: [03:17:28] should not be silent -7: [03:17:28] should not be silent -7: [03:17:28] should not be silent -7: [03:17:28] should not be silent -7: [03:17:28] should not be silent +7: [12:24:52] should not be silent +7: [12:24:52] should not be silent +7: Randomness seeded to: 3453695633 +7: [12:24:52] should not be silent +7: [12:24:52] should not be silent +7: [12:24:52] should not be silent +7: [12:24:52] should not be silent +7: [12:24:52] should not be silent +7: [12:24:52] should not be silent +7: [12:24:52] should not be silent +7: [12:24:52] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: @@ -11223,11 +11254,11 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except - 1/222 Test #4: testRDValue ............................ Passed 0.08 sec - 2/222 Test #6: dictTestsCatch ......................... Passed 0.07 sec - 3/222 Test #7: logTestsCatch .......................... Passed 0.06 sec - 4/222 Test #8: testDataStructs ........................ Passed 0.06 sec - 5/222 Test #9: testFPB ................................ Passed 0.06 sec + 1/222 Test #4: testRDValue ............................ Passed 0.18 sec + 2/222 Test #6: dictTestsCatch ......................... Passed 0.14 sec + 3/222 Test #7: logTestsCatch .......................... Passed 0.13 sec + 4/222 Test #8: testDataStructs ........................ Passed 0.11 sec + 5/222 Test #9: testFPB ................................ Passed 0.08 sec test 13 Start 13: pySparseIntVect @@ -11258,6 +11289,72 @@ 17: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry/geometryTestsCatch 17: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry 17: Test timeout computed to be: 1500 +15: **************************************** +15: testPointND +15: **************************************** +15: testPointOps3D +15: **************************************** +15: testPointOps2D +15: **************************************** +15: test12D +15: ref1: 3.55463 1.3476 ref2: 1.48481 1.3495 +15: pt1: 4.25056 3.0079 pt2: 2.20532 3.36268 +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: **************************************** +16: *********************************************************** +16: Testing Grid +16: --------------------------------- +16: testUniformGrid1 +16: +16: --------------------------------- +16: testUniformGrid2 +16: +16: --------------------------------- +16: testUniformGridPickling +16: +16: --------------------------------- +16: testGridOps +16: +16: --------------------------------- +16: testUniformGridIndexing +16: + 6/222 Test #10: testMultiFPB ........................... Passed 0.17 sec + 7/222 Test #15: testTransforms ......................... Passed 0.08 sec + 8/222 Test #16: testGrid ............................... Passed 0.05 sec +test 18 + Start 18: testPyGeometry + +18: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/testGeometry.py" +18: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap +18: Test timeout computed to be: 1500 +test 19 + Start 19: testMatrices + +19: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/testMatrices +19: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics +19: Test timeout computed to be: 1500 +test 20 + Start 20: testConrec + +20: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/testConrec +20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics +20: Test timeout computed to be: 1500 +17: Randomness seeded to: 1819051725 +17: =============================================================================== +17: All tests passed (50 assertions in 5 test cases) +17: 1: cyclosporine a 1: RDKit 2D 1: @@ -11498,6 +11595,30 @@ 1: 9 10 1 0 1: M END 1: +19: [12:24:52] ----------------------------------------- +19: [12:24:52] Testing RDNumerics: vectors and matrices Code +19: [12:24:52] --------------------------------------- +19: [12:24:52] test1Vector +19: [12:24:52] --------------------------------------- +19: [12:24:52] test2Matrix +19: [12:24:52] --------------------------------------- +19: [12:24:52] test3SquareMatrix +19: [12:24:52] --------------------------------------- +19: [12:24:52] test4SymmMatrix + 9/222 Test #17: geometryTestsCatch ..................... Passed 0.10 sec + 10/222 Test #19: testMatrices ........................... Passed 0.06 sec +test 21 + Start 21: testAlignment + +21: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment +21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment +21: Test timeout computed to be: 1500 +test 22 + Start 22: pyAlignment + +22: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/testAlignment.py" +22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap +22: Test timeout computed to be: 1500 1: admntn 1: RDKit 2D 1: @@ -11526,68 +11647,6 @@ 1: 10 2 1 0 1: M END 1: -15: **************************************** -15: testPointND -15: **************************************** -15: testPointOps3D -15: **************************************** -15: testPointOps2D -15: **************************************** -15: test12D -15: ref1: 3.0212 4.39026 ref2: 4.36883 0.978755 -15: pt1: 2.33073 4.97832 pt2: 2.04149 1.38144 -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: **************************************** -16: *********************************************************** -16: Testing Grid -16: --------------------------------- -16: testUniformGrid1 -16: -16: --------------------------------- -16: testUniformGrid2 -16: -16: --------------------------------- -16: testUniformGridPickling -16: -16: --------------------------------- -16: testGridOps -16: -16: --------------------------------- -16: testUniformGridIndexing -16: - 6/222 Test #10: testMultiFPB ........................... Passed 0.12 sec - 7/222 Test #15: testTransforms ......................... Passed 0.03 sec - 8/222 Test #16: testGrid ............................... Passed 0.01 sec -test 18 - Start 18: testPyGeometry - -18: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/testGeometry.py" -18: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Geometry/Wrap -18: Test timeout computed to be: 1500 -test 19 - Start 19: testMatrices - -19: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/testMatrices -19: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics -19: Test timeout computed to be: 1500 -test 20 - Start 20: testConrec - -20: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/testConrec -20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics -20: Test timeout computed to be: 1500 1: github 4845 - nan coordinates but no crash 1: RDKit 2D 1: @@ -11680,42 +11739,7 @@ 1: 30 11 1 0 1: M END 1: -17: Randomness seeded to: 2258685012 -17: =============================================================================== -17: All tests passed (50 assertions in 5 test cases) -17: -19: [03:17:28] ----------------------------------------- -19: [03:17:28] Testing RDNumerics: vectors and matrices Code -19: [03:17:28] --------------------------------------- -19: [03:17:28] test1Vector -19: [03:17:28] --------------------------------------- -19: [03:17:28] test2Matrix -19: [03:17:28] --------------------------------------- -19: [03:17:28] test3SquareMatrix -19: [03:17:28] --------------------------------------- -19: [03:17:28] test4SymmMatrix - 9/222 Test #1: testCoordGen ........................... Passed 0.21 sec - 10/222 Test #17: geometryTestsCatch ..................... Passed 0.05 sec - 11/222 Test #19: testMatrices ........................... Passed 0.03 sec -test 21 - Start 21: testAlignment - -21: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/testAlignment -21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment -21: Test timeout computed to be: 1500 -test 22 - Start 22: pyAlignment - -22: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/testAlignment.py" -22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Alignment/Wrap -22: Test timeout computed to be: 1500 -test 23 - Start 23: testOptimizer - -23: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer -23: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer -23: Test timeout computed to be: 1500 -20: Randomness seeded to: 3087746722 +20: Randomness seeded to: 2165858414 20: 20: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 20: testConrec is a Catch2 v3.4.0 host application. @@ -11748,14 +11772,8 @@ 21: --------------------------------------- 21: testReflection 21: --------------------------------------- -23: ------------------------------------- -23: Testing linear search. -23: done -23: ------------------------------------- -23: Testing BFGS optimization. -23: done - 12/222 Test #20: testConrec .............................***Failed 0.05 sec -Randomness seeded to: 3087746722 + 11/222 Test #20: testConrec .............................***Failed 0.09 sec +Randomness seeded to: 2165858414 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ testConrec is a Catch2 v3.4.0 host application. @@ -11778,14 +11796,27 @@ assertions: 179 | 178 passed | 1 failed - 13/222 Test #21: testAlignment .......................... Passed 0.03 sec - 14/222 Test #23: testOptimizer .......................... Passed 0.02 sec + 12/222 Test #21: testAlignment .......................... Passed 0.05 sec +test 23 + Start 23: testOptimizer + +23: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer/testOptimizer +23: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/Numerics/Optimizer +23: Test timeout computed to be: 1500 test 24 Start 24: testUFFForceField 24: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/UFF/testUFFForceField 24: Working Directory: /build/reproducible-path/rdkit-202309.3/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 + 13/222 Test #1: testCoordGen ........................... Passed 0.53 sec + 14/222 Test #23: testOptimizer .......................... Passed 0.05 sec test 25 Start 25: testMMFFForceField @@ -11798,16 +11829,6 @@ 26: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/testConstraints.py" 26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ForceField/Wrap 26: Test timeout computed to be: 1500 -12: ...... -12: ---------------------------------------------------------------------- -12: Ran 6 tests in 0.002s -12: -12: OK -2: .... -2: ---------------------------------------------------------------------- -2: Ran 4 tests in 0.021s -2: -2: OK 24: ------------------------------------- 24: Unit tests for force field basics. 24: done @@ -11856,39 +11877,47 @@ 24: Unit tests for all UFF constraint terms. 25: ------------------------------------- 25: Official MMFF validation suite. +24: done +24: ------------------------------------- +24: Unit tests for copying UFF ForceFields. +24: done +24: ------------------------------------- +24: Unit test for UFF butane scan. 13: ......... 13: ---------------------------------------------------------------------- -13: Ran 9 tests in 0.005s +13: Ran 9 tests in 0.021s 13: 13: OK -24: done -24: ------------------------------------- -24: Unit tests for copying UFF ForceFields. - 15/222 Test #2: pyCoordGen ............................. Passed 0.36 sec - 16/222 Test #12: pyDiscreteValueVect .................... Passed 0.30 sec +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... +2: .... +2: ---------------------------------------------------------------------- +2: Ran 4 tests in 0.051s +2: +2: OK +12: ...... +12: ---------------------------------------------------------------------- +12: Ran 6 tests in 0.018s +12: +12: OK +18: ........... +18: ---------------------------------------------------------------------- +18: Ran 11 tests in 0.035s +18: +18: OK +18: Testing Geometry wrapper + 15/222 Test #13: pySparseIntVect ........................ Passed 0.76 sec test 27 Start 27: testDistGeom 27: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/testDistGeom 27: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom 27: Test timeout computed to be: 1500 -test 28 - Start 28: pyDistGeom - -28: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" -28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap -28: Test timeout computed to be: 1500 -24: done -24: ------------------------------------- -24: Unit test for UFF butane scan. -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... 14: ......... 14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.060s +14: Ran 9 tests in 0.093s 14: 14: OK -3: dynamic boost any:0.239614 s 27: *********************************************************** 27: test1 27: *********************************************************** @@ -11900,13 +11929,26 @@ 27: 1 1 1 0 27: *********************************************************** 27: - 17/222 Test #27: testDistGeom ........................... Passed 0.03 sec + 16/222 Test #27: testDistGeom ........................... Passed 0.05 sec +test 28 + Start 28: pyDistGeom + +28: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" +28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DistGeom/Wrap +28: Test timeout computed to be: 1500 + 17/222 Test #2: pyCoordGen ............................. Passed 1.05 sec test 29 Start 29: graphmolTest1 29: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTest1 29: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 29: Test timeout computed to be: 1500 +22: ..... +22: ---------------------------------------------------------------------- +22: Ran 5 tests in 0.001s +22: +22: OK +22: Testing Alignment Wrapper code: 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 @@ -11916,7 +11958,7 @@ 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: [03:17:29] +29: 8 22 Ti chg: 0 deg: 1 exp: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -11934,7 +11976,7 @@ 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: [03:17:29] +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -11943,7 +11985,7 @@ 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: -29: [03:17:29] +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -11952,7 +11994,7 @@ 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: -29: [03:17:29] +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -11961,7 +12003,7 @@ 29: Failed Expression: atomIdx1 != atomIdx2 29: **** 29: -29: [03:17:29] +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -11970,7 +12012,7 @@ 29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 29: **** 29: -29: [03:17:29] +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -11979,9 +12021,17 @@ 29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 29: **** 29: -29: [03:17:29] Explicit valence for atom # 0 B, 4, is greater than permitted -29: [03:17:29] Explicit valence for atom # 0 B, 5, is greater than permitted -29: [03:17:29] +29: [12:24:53] Explicit valence for atom # 0 B, 4, is greater than permitted +29: [12:24:53] Explicit valence for atom # 0 B, 5, is greater than permitted +3: dynamic boost any:0.24896 s + 18/222 Test #18: testPyGeometry ......................... Passed 0.81 sec +test 30 + Start 30: graphmolcpTest + +30: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest +30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +30: Test timeout computed to be: 1500 +29: [12:24:53] 29: 29: **** 29: Post-condition Violation @@ -11990,31 +12040,31 @@ 29: Failed Expression: anum > -1 29: **** 29: -29: [03:17:29] ------------------------------------- -29: [03:17:29] Test github381: thread-safe initialization of the periodic table -3: static RDAny:0.030244 s - 18/222 Test #13: pySparseIntVect ........................ Passed 0.35 sec -test 30 - Start 30: graphmolcpTest - -30: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolcpTest -30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -30: Test timeout computed to be: 1500 -30: -30: -30: -30: COPY - 19/222 Test #14: pyFPB .................................. Passed 0.36 sec +29: [12:24:53] ------------------------------------- +29: [12:24:53] Test github381: thread-safe initialization of the periodic table +24: done + 19/222 Test #24: testUFFForceField ...................... Passed 0.68 sec test 31 Start 31: graphmolqueryTest 31: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolqueryTest 31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 31: Test timeout computed to be: 1500 -29: [03:17:29] done -29: [03:17:29] ------------------------------------- -29: [03:17:29] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [03:17:29] +30: +30: +30: +30: COPY + 20/222 Test #14: pyFPB .................................. Passed 0.94 sec +test 32 + Start 32: graphmolMolOpsTest + +32: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest +32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +32: Test timeout computed to be: 1500 +29: [12:24:53] done +29: [12:24:53] ------------------------------------- +29: [12:24:53] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -12023,7 +12073,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [03:17:29] +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -12032,10 +12082,10 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [03:17:29] done -29: [03:17:29] ------------------------------------- -29: [03:17:29] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [03:17:29] +29: [12:24:53] done +29: [12:24:53] ------------------------------------- +29: [12:24:53] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -12044,7 +12094,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [03:17:29] +29: [12:24:53] 29: 29: **** 29: Pre-condition Violation @@ -12053,136 +12103,138 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [03:17:29] done -29: [03:17:29] ------------------------------------- -29: [03:17:29] Test github1453: RWMol.clear() should reset the numBonds count. -29: [03:17:29] done -29: [03:17:29] ------------------------------------- -29: [03:17:29] Test range-based for loops. -29: [03:17:29] done -29: [03:17:29] ------------------------------------- -29: [03:17:29] Test github1642: Atom index type is too low for big molecules. - 20/222 Test #30: graphmolcpTest ......................... Passed 0.03 sec -test 32 - Start 32: graphmolMolOpsTest - -32: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMolOpsTest -32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -32: Test timeout computed to be: 1500 -22: ..... -22: ---------------------------------------------------------------------- -22: Ran 5 tests in 0.001s -22: -22: OK -22: Testing Alignment Wrapper code: -31: [03:17:29] ---------------------- Test1 -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test2 -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test3 -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test4 -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test5 -31: [03:17:29] Done! -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test issue 2892580 -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test github issue 53: query molecules not matching [R] -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test queries using qualifiers instead of == -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test extra atom queries -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test extra bond queries -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test num heteroatom neighbor queries -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test atom type queries -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -31: [03:17:29] Done! -31: [03:17:29] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -31: [03:17:29] Done! - 21/222 Test #31: graphmolqueryTest ...................... Passed 0.03 sec +29: [12:24:53] done +29: [12:24:53] ------------------------------------- +29: [12:24:53] Test github1453: RWMol.clear() should reset the numBonds count. +29: [12:24:53] done +29: [12:24:53] ------------------------------------- +29: [12:24:53] Test range-based for loops. +29: [12:24:53] done +29: [12:24:53] ------------------------------------- +29: [12:24:53] Test github1642: Atom index type is too low for big molecules. +3: static RDAny:0.030227 s +31: [12:24:53] ---------------------- Test1 + 21/222 Test #12: pyDiscreteValueVect .................... Passed 1.00 sec + 22/222 Test #30: graphmolcpTest ......................... Passed 0.06 sec test 33 Start 33: graphmoltestChirality 33: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestChirality 33: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 33: Test timeout computed to be: 1500 -32: 1 1 2 -32: 1 1 1 -32: 2 1 0.75 -32: path: 2 -18: ........... -18: ---------------------------------------------------------------------- -18: Ran 11 tests in 0.023s -18: -18: OK -18: Testing Geometry wrapper -33: -------------------------- -33: -------------------------- -33: C/C=C/C(C)Cl -32: [03:17:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -32: [03:17:29] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored -32: [03:17:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -33: [03:17:29] Conflicting single bond directions around double bond at index 2. -33: [03:17:29] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [03:17:29] Conflicting single bond directions around double bond at index 4. -33: [03:17:29] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [03:17:29] Conflicting single bond directions around double bond at index 15. -33: [03:17:29] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [03:17:29] Conflicting single bond directions around double bond at index 2. -33: [03:17:29] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [03:17:29] Conflicting single bond directions around double bond at index 1. -33: [03:17:29] BondStereo set to STEREONONE and single bond directions set to NONE. -32: [03:17:29] Explicit valence for atom # 0 B, 5, is greater than permitted -32: [03:17:29] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [03:17:29] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [03:17:29] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [03:17:29] Explicit valence for atom # 1 Si, 7, is greater than permitted -33: -------------------------------------------------- - 22/222 Test #33: graphmoltestChirality .................. Passed 0.05 sec test 34 Start 34: graphmoltestPickler 34: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPickler 34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 34: Test timeout computed to be: 1500 -24: done - 23/222 Test #22: pyAlignment ............................ Passed 0.33 sec - 24/222 Test #24: testUFFForceField ...................... Passed 0.30 sec +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test2 +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test3 +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test4 +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test5 +31: [12:24:53] Done! +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test issue 2892580 +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test github issue 53: query molecules not matching [R] +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test queries using qualifiers instead of == +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test extra atom queries +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test extra bond queries +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test num heteroatom neighbor queries +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test atom type queries +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +31: [12:24:53] Done! +31: [12:24:53] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +31: [12:24:53] Done! + 23/222 Test #31: graphmolqueryTest ...................... Passed 0.08 sec test 35 Start 35: graphmoltestPicklerGlobalSetting 35: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting 35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 35: Test timeout computed to be: 1500 + 24/222 Test #22: pyAlignment ............................ Passed 0.83 sec test 36 Start 36: graphmolIterTest 36: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolIterTest 36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 36: Test timeout computed to be: 1500 -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing String Pickle Roundtrips. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing reading existing pickle file (v2). -35: [03:17:29] done - 25/222 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.04 sec +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing String Pickle Roundtrips. +32: 1 1 2 +32: 1 1 1 +32: 2 1 0.75 +32: path: 2 +32: [12:24:53] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +32: [12:24:53] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored +32: [12:24:53] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +33: -------------------------- +33: -------------------------- +33: C/C=C/C(C)Cl +35: [12:24:53] done + 25/222 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.05 sec test 37 Start 37: hanoiTest 37: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/hanoiTest 37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 37: Test timeout computed to be: 1500 -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing combining molecules using pickles. +33: [12:24:53] Conflicting single bond directions around double bond at index 2. +33: [12:24:53] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [12:24:53] Conflicting single bond directions around double bond at index 4. +33: [12:24:53] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [12:24:53] Conflicting single bond directions around double bond at index 15. +33: [12:24:53] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [12:24:53] Conflicting single bond directions around double bond at index 2. +33: [12:24:53] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [12:24:53] Conflicting single bond directions around double bond at index 1. +33: [12:24:53] BondStereo set to STEREONONE and single bond directions set to NONE. +32: [12:24:53] Explicit valence for atom # 0 B, 5, is greater than permitted +32: [12:24:53] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [12:24:53] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [12:24:53] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [12:24:53] Explicit valence for atom # 1 Si, 7, is greater than permitted +33: -------------------------------------------------- + 26/222 Test #33: graphmoltestChirality .................. Passed 0.12 sec + 27/222 Test #36: graphmolIterTest ....................... Passed 0.06 sec +test 38 + Start 38: graphmolMemTest1 + +38: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 +38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 +test 39 + Start 39: resMolSupplierTest + +39: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest +39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing reading existing pickle file (v2). + 28/222 Test #38: graphmolMemTest1 ....................... Passed 0.06 sec +test 40 + Start 40: molBundleTest + +40: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest +40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] 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 @@ -12199,53 +12251,45 @@ 34: 4 4->5 order: 1 conj?: 0 aromatic?: 0 34: 5 5->6 order: 1 conj?: 0 aromatic?: 0 34: 6 6->3 order: 1 conj?: 0 aromatic?: 0 -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing Issue164: Roundtrip Pickle Failure. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing Issue219: Pickle Failure with Conformations. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing Issue220: Pickle problems with bond stereochemistry. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing query serialization. -34: [03:17:29] C=[$(C=O)] -34: [03:17:29] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing radical handling in pickles. -34: [03:17:29] done -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing sf.net issue 2788233. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing sf.net issue 3202580. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing Issue164: Roundtrip Pickle Failure. + 29/222 Test #40: molBundleTest .......................... Passed 0.07 sec +test 41 + Start 41: testSGroup + +41: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup +41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing Issue219: Pickle Failure with Conformations. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing Issue220: Pickle problems with bond stereochemistry. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing query serialization. +34: [12:24:53] C=[$(C=O)] +34: [12:24:53] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing radical handling in pickles. +34: [12:24:53] done +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing sf.net issue 2788233. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing sf.net issue 3202580. 34: mass! 13.0034 -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing sf.net issue 3316407. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing sf.net issue 3496759. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing sf.net issue 3316407. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing sf.net issue 3496759. 34: smi match: *C *C -32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 - 26/222 Test #18: testPyGeometry ......................... Passed 0.45 sec - 27/222 Test #36: graphmolIterTest ....................... Passed 0.04 sec -test 38 - Start 38: graphmolMemTest1 - -38: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolMemTest1 -38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 -test 39 - Start 39: resMolSupplierTest - -39: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/resMolSupplierTest -39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 34: smi match: **=* **=* 34: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O 34: smi match: *OS(=O)OC *OS(=O)OC @@ -12264,6 +12308,7 @@ 34: smi match: NNC=O NNC=O 34: smi match: * * 34: smi match: C=P C=P +32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 34: smi match: CC(=N)Cl CC(=N)Cl 34: smi match: N=O N=O 34: smi match: ** ** @@ -12376,6 +12421,8 @@ 34: smi match: N=C(N)O N=C(N)O 34: smi match: N=C(N)C(=N)S N=C(N)C(=N)S 34: smi match: *C=N *C=N +32: [12:24:53] non-ring atom 0 marked aromatic +32: [12:24:53] non-ring atom 0 marked aromatic 34: smi match: N=CC=O N=CC=O 34: smi match: N=CS N=CS 34: smi match: N=C=N N=C=N @@ -12422,6 +12469,16 @@ 34: smi match: O=C(S)S O=C(S)S 34: smi match: N=C(S)S N=C(S)S 34: smi match: N=C(=N)S N=C(=N)S +32: [12:24:53] Conflicting single bond directions around double bond at index 17. +32: [12:24:53] BondStereo set to STEREONONE and single bond directions set to NONE. +32: starting ring finding + 30/222 Test #41: testSGroup ............................. Passed 0.09 sec +test 42 + Start 42: test-valgrind + +42: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind +42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 34: smi match: O=N=O O=N=O 34: smi match: O=NO O=NO 34: smi match: ONO ONO @@ -12469,37 +12526,6 @@ 34: smi match: OO OO 34: smi match: O~Cl(~O)~O O~Cl(~O)~O 34: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O -32: [03:17:29] non-ring atom 0 marked aromatic -32: [03:17:29] non-ring atom 0 marked aromatic -32: [03:17:29] Conflicting single bond directions around double bond at index 17. -32: [03:17:29] 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 -26: ...[03:17:29] Molecule does not have explicit Hs. Consider calling AddHs() -26: [03:17:29] -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: -28: ...... -28: ---------------------------------------------------------------------- -28: Ran 6 tests in 0.001s -28: -28: OK - 28/222 Test #38: graphmolMemTest1 ....................... Passed 0.04 sec -test 40 - Start 40: molBundleTest - -40: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/molBundleTest -40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 34: smi match: [OH]~C(~O)~O [OH]~C(~O)~O 34: smi match: *N *N 34: smi match: *P *P @@ -12520,6 +12546,13 @@ 34: smi match: *C(=O)OC=O *C(=O)OC=O 34: smi match: C=CC#N C=CC#N 34: smi match: C=CC=O C=CC=O +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 34: smi match: CC=CC(C)=O CC=CC(C)=O 34: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 34: smi match: C#CC#N C#CC#N @@ -12580,6 +12613,21 @@ 34: smi match: cC(=N)[NH2] cC(=N)[NH2] 34: smi match: O=CN[OH] O=CN[OH] 34: smi match: NN NN +32: done +32: starting sanitization +32: done + 31/222 Test #42: test-valgrind .......................... Passed 0.05 sec +test 43 + Start 43: graphmolTestsCatch + +43: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch +43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 +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 34: smi match: * * 34: smi match: *OP(=O)O* *OP(=O)O* 34: smi match: * * @@ -12626,6 +12674,8 @@ 34: smi match: **:*cF **:*cF 34: smi match: cB([OH])[OH] cB([OH])[OH] 34: smi match: N~N~N N~N~N +32: [12:24:53] WARNING: not removing hydrogen atom with dummy atom neighbors +32: ------------------------------- 34: smi match: *N=N* *N=N* 34: smi match: *CC[OH] *CC[OH] 34: smi match: *CC[OH] *CC[OH] @@ -12645,6 +12695,16 @@ 34: smi match: SS SS 34: smi match: * * 34: smi match: *=* *=* +32: [12:24:53] Explicit valence for atom # 0 N, 4, is greater than permitted +32: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +28: ...... +28: ---------------------------------------------------------------------- +28: Ran 6 tests in 0.001s +28: +28: OK +32: [12:24:53] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +32: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [12:24:53] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 34: smi match: *=* *=* 34: smi match: *=* *=* 34: smi match: *=* *=* @@ -12695,6 +12755,17 @@ 34: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 34: smi match: *C(*)=S *C(*)=S 34: smi match: *OC(*)=S *OC(*)=S +32: [12:24:53] WARNING: not removing hydrogen atom with dummy atom neighbors +26: ...[12:24:53] Molecule does not have explicit Hs. Consider calling AddHs() +26: [12:24:53] +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: smi match: * * 34: smi match: C[SH] C[SH] 34: smi match: c[SH] c[SH] @@ -12702,139 +12773,88 @@ 34: smi match: * * 34: smi match: ***** ***** 34: smi match: NC(N)=O NC(N)=O -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing sf.net issue 280. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing sf.net issue 285. -34: [03:17:29] done -34: [03:17:29] done -34: [03:17:29] done -34: [03:17:29] done -34: [03:17:29] done -34: [03:17:29] done -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing Github2441: Add RDProps interface to Conformers. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing Issue2510: Pickle Confs as double. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing loading pickled mols with conformers -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing conformer reading/writing options -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing property reading options -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing property reading options -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing boost::serialization integration -34: [03:17:29] done -34: [03:17:29] ------------------------------------- -34: [03:17:29] Testing github issue 6036 -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 -32: starting sanitization - 29/222 Test #34: graphmoltestPickler .................... Passed 0.14 sec -test 41 - Start 41: testSGroup - -41: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/testSGroup -41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 -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: [03:17:29] WARNING: not removing hydrogen atom with dummy atom neighbors -32: ------------------------------- -32: [03:17:29] Explicit valence for atom # 0 N, 4, is greater than permitted -32: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [03:17:29] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -32: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [03:17:29] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -32: [03:17:29] WARNING: not removing hydrogen atom with dummy atom neighbors - 30/222 Test #28: pyDistGeom ............................. Passed 0.36 sec - 31/222 Test #40: molBundleTest .......................... Passed 0.08 sec -test 42 - Start 42: test-valgrind - -42: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/test-valgrind -42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 -test 43 - Start 43: graphmolTestsCatch - -43: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolTestsCatch -43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 - 32/222 Test #41: testSGroup ............................. Passed 0.09 sec - 33/222 Test #42: test-valgrind .......................... Passed 0.04 sec +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing sf.net issue 280. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing sf.net issue 285. +34: [12:24:53] done +34: [12:24:53] done +34: [12:24:53] done +34: [12:24:53] done +34: [12:24:53] done +34: [12:24:53] done +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing Github2441: Add RDProps interface to Conformers. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing Issue2510: Pickle Confs as double. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing loading pickled mols with conformers +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing conformer reading/writing options +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing property reading options +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing property reading options +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing boost::serialization integration +34: [12:24:53] done +34: [12:24:53] ------------------------------------- +34: [12:24:53] Testing github issue 6036 + 32/222 Test #34: graphmoltestPickler .................... Passed 0.44 sec test 44 Start 44: graphmolOrganometallicsCatch 44: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch 44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 44: Test timeout computed to be: 1500 -test 45 - Start 45: graphmolSGroupCatch - -45: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch -45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 -43: Randomness seeded to: 2285454947 -43: [03:17:29] WARNING: not removing hydrogen atom without neighbors -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:17:29] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 1 N, 6, is greater than permitted -43: [03:17:29] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [03:17:29] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [03:17:29] non-ring atom 2 marked aromatic -43: [03:17:29] non-ring atom 2 marked aromatic -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [03:17:29] Explicit valence for atom # 1 O, 3, is greater than permitted -43: [03:17:29] Explicit valence for atom # 4 F, 2, is greater than permitted -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 6 7 8 -43: [03:17:29] Explicit valence for atom # 1 C, 5, is greater than permitted -43: [03:17:29] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [03:17:29] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [03:17:29] WARNING: not removing hydrogen atom with wedged bond -43: [03:17:29] WARNING: not removing hydrogen atom without neighbors -43: [03:17:29] WARNING: not removing hydrogen atom without neighbors -43: [03:17:29] WARNING: not removing hydrogen atom without neighbors -43: [03:17:29] WARNING: not removing hydrogen atom without neighbors -45: Randomness seeded to: 2311178331 -45: =============================================================================== -45: All tests passed (120 assertions in 6 test cases) -45: -43: [03:17:29] Unreasonable formal charge on hydrogen # 0. -43: [03:17:29] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [03:17:29] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [03:17:29] +43: Randomness seeded to: 4061307347 +43: [12:24:53] WARNING: not removing hydrogen atom without neighbors +43: [12:24:53] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:24:53] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:24:53] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:24:53] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:24:53] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:24:53] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [12:24:53] Explicit valence for atom # 1 N, 6, is greater than permitted +43: [12:24:53] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [12:24:53] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [12:24:53] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [12:24:53] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [12:24:53] non-ring atom 2 marked aromatic +43: [12:24:53] non-ring atom 2 marked aromatic +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [12:24:53] Explicit valence for atom # 1 O, 3, is greater than permitted +43: [12:24:53] Explicit valence for atom # 4 F, 2, is greater than permitted +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 6 7 8 +43: [12:24:53] Explicit valence for atom # 1 C, 5, is greater than permitted +43: [12:24:53] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [12:24:53] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [12:24:53] WARNING: not removing hydrogen atom with wedged bond +43: [12:24:53] WARNING: not removing hydrogen atom without neighbors +43: [12:24:53] WARNING: not removing hydrogen atom without neighbors +43: [12:24:53] WARNING: not removing hydrogen atom without neighbors +43: [12:24:53] WARNING: not removing hydrogen atom without neighbors +43: [12:24:53] Unreasonable formal charge on hydrogen # 0. +43: [12:24:53] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [12:24:53] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12843,7 +12863,7 @@ 43: Failed Expression: at 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12852,7 +12872,7 @@ 43: Failed Expression: dp_mol 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12861,7 +12881,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12870,7 +12890,7 @@ 43: Failed Expression: at 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12879,7 +12899,7 @@ 43: Failed Expression: dp_mol 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12888,7 +12908,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12897,7 +12917,7 @@ 43: Failed Expression: at 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12906,7 +12926,7 @@ 43: Failed Expression: dp_mol 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12915,7 +12935,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12924,7 +12944,7 @@ 43: Failed Expression: atom_pin 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12933,7 +12953,7 @@ 43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12942,11 +12962,11 @@ 43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 43: **** 43: -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:17:29] WARNING: not removing hydrogen atom without neighbors -43: [03:17:29] Explicit valence for atom # 1 F greater than permitted -43: [03:17:29] +43: [12:24:53] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:24:53] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:24:53] WARNING: not removing hydrogen atom without neighbors +43: [12:24:53] Explicit valence for atom # 1 F greater than permitted +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12955,7 +12975,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12964,7 +12984,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12973,7 +12993,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [03:17:29] +43: [12:24:53] 43: 43: **** 43: Pre-condition Violation @@ -12982,254 +13002,296 @@ 43: Failed Expression: 0 43: **** 43: -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 - 34/222 Test #45: graphmolSGroupCatch .................... Passed 0.03 sec +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [12:24:53] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:24:54] Unusual charge on atom 0 number of radical electrons set to zero +43: [12:24:54] Unusual charge on atom 0 number of radical electrons set to zero +43: [12:24:54] Unusual charge on atom 0 number of radical electrons set to zero +43: [12:24:54] non-ring atom 0 marked aromatic +43: [12:24:54] non-ring atom 0 marked aromatic +43: [12:24:54] Explicit valence for atom # 1 C, 5, is greater than permitted +43: [12:24:54] Explicit valence for atom # 9 C, 5, is greater than permitted +43: [12:24:54] Explicit valence for atom # 3 N, 4, is greater than permitted +43: [12:24:54] Explicit valence for atom # 15 C, 5, is greater than permitted +43: [12:24:54] Explicit valence for atom # 11 C, 5, is greater than permitted +43: [12:24:54] Explicit valence for atom # 9 C, 5, is greater than permitted +43: [12:24:54] Explicit valence for atom # 9 C, 5, is greater than permitted +43: [12:24:54] Explicit valence for atom # 9 C, 6, is greater than permitted +43: [12:24:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [12:24:54] Can't kekulize mol. Unkekulized atoms: 7 +43: [12:24:54] Can't kekulize mol. Unkekulized atoms: 3 +43: [12:24:54] Can't kekulize mol. Unkekulized atoms: 3 7 +43: [12:24:54] Can't kekulize mol. Unkekulized atoms: 3 7 +43: [12:24:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [12:24:54] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. + 33/222 Test #28: pyDistGeom ............................. Passed 0.76 sec +test 45 + Start 45: graphmolSGroupCatch + +45: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolSGroupCatch +45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 +44: Randomness seeded to: 3959557680 +44: =============================================================================== +44: All tests passed (62 assertions in 6 test cases) +44: + 34/222 Test #44: graphmolOrganometallicsCatch ........... Passed 0.14 sec test 46 Start 46: graphmolAdjustQueryCatch 46: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch 46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 46: Test timeout computed to be: 1500 -43: [03:17:29] Unusual charge on atom 0 number of radical electrons set to zero -43: [03:17:29] Unusual charge on atom 0 number of radical electrons set to zero -43: [03:17:29] Unusual charge on atom 0 number of radical electrons set to zero -43: [03:17:29] non-ring atom 0 marked aromatic -43: [03:17:29] non-ring atom 0 marked aromatic -43: [03:17:29] Explicit valence for atom # 1 C, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 9 C, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 3 N, 4, is greater than permitted -43: [03:17:29] Explicit valence for atom # 15 C, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 11 C, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 9 C, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 9 C, 5, is greater than permitted -43: [03:17:29] Explicit valence for atom # 9 C, 6, is greater than permitted -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 7 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 3 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 3 7 -43: [03:17:29] Can't kekulize mol. Unkekulized atoms: 3 7 -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [03:17:29] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: Randomness seeded to: 1812613627 -44: =============================================================================== -44: All tests passed (62 assertions in 6 test cases) -44: - 35/222 Test #44: graphmolOrganometallicsCatch ........... Passed 0.06 sec +45: Randomness seeded to: 1002248677 +45: =============================================================================== +45: All tests passed (120 assertions in 6 test cases) +45: + 35/222 Test #45: graphmolSGroupCatch .................... Passed 0.08 sec test 47 Start 47: chiralityTestsCatch 47: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/chiralityTestsCatch 47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 47: Test timeout computed to be: 1500 -43: [03:17:29] Explicit valence for atom # 1 O, 3, is greater than permitted -43: [03:17:29] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -43: [03:17:29] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -43: [03:17:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -43: [03:17:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +43: [12:24:54] Explicit valence for atom # 1 O, 3, is greater than permitted +43: [12:24:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +43: [12:24:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +43: [12:24:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +43: [12:24:54] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 43: =============================================================================== 43: All tests passed (1630 assertions in 89 test cases) 43: - 36/222 Test #43: graphmolTestsCatch ..................... Passed 0.10 sec + 36/222 Test #43: graphmolTestsCatch ..................... Passed 0.28 sec test 48 Start 48: canonTestsCatch 48: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/canonTestsCatch 48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 48: Test timeout computed to be: 1500 -47: Randomness seeded to: 3171587276 -47: [03:17:29] unable to set wavy bonds for double bonds: 3 -26: ......[03:17:29] Molecule does not have explicit Hs. Consider calling AddHs() -47: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -47: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -46: Randomness seeded to: 988509490 +46: Randomness seeded to: 290510101 46: =============================================================================== 46: All tests passed (281 assertions in 10 test cases) 46: -48: Randomness seeded to: 869947282 -48: =============================================================================== -48: All tests passed (137 assertions in 7 test cases) -48: - 37/222 Test #46: graphmolAdjustQueryCatch ............... Passed 0.06 sec - 38/222 Test #48: canonTestsCatch ........................ Passed 0.02 sec + 37/222 Test #46: graphmolAdjustQueryCatch ............... Passed 0.12 sec test 49 Start 49: moliteratorTestsCatch 49: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/moliteratorTestsCatch 49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 49: Test timeout computed to be: 1500 +48: Randomness seeded to: 1917752358 +48: =============================================================================== +48: All tests passed (137 assertions in 7 test cases) +48: + 38/222 Test #48: canonTestsCatch ........................ Passed 0.08 sec test 50 Start 50: queryTestsCatch 50: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/queryTestsCatch 50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 50: Test timeout computed to be: 1500 -47: [03:17:29] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -47: [03:17:29] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -47: [03:17:29] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored -47: [03:17:29] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored -47: [03:17:29] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -47: =============================================================================== -47: All tests passed (1845 assertions in 63 test cases) -47: -26: [03:17:29] -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: -49: Randomness seeded to: 620592934 +47: Randomness seeded to: 1540804454 +47: [12:24:54] unable to set wavy bonds for double bonds: 3 +47: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +47: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +49: Randomness seeded to: 2992507502 49: =============================================================================== 49: All tests passed (14 assertions in 4 test cases) 49: - 39/222 Test #47: chiralityTestsCatch .................... Passed 0.06 sec - 40/222 Test #49: moliteratorTestsCatch .................. Passed 0.02 sec + 39/222 Test #49: moliteratorTestsCatch .................. Passed 0.07 sec test 51 Start 51: molbundleTestsCatch 51: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/molbundleTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 51: Test timeout computed to be: 1500 +26: ......[12:24:54] Molecule does not have explicit Hs. Consider calling AddHs() +26: [12:24:54] +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: +3: dynamic RDAny:0.234015 s +3: static RDValue:0 s +50: Randomness seeded to: 3280007820 +50: =============================================================================== +50: All tests passed (10 assertions in 1 test case) +50: + 40/222 Test #50: queryTestsCatch ........................ Passed 0.06 sec test 52 Start 52: pickleTestsCatch 52: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/pickleTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol 52: Test timeout computed to be: 1500 -50: Randomness seeded to: 83122868 -50: =============================================================================== -50: All tests passed (10 assertions in 1 test case) -50: -3: dynamic RDAny:0.233738 s -3: static RDValue:0 s -32: [03:17:29] Maximum BFS search size exceeded. -32: This is likely due to a highly symmetric fused ring system. -51: Randomness seeded to: 1779859039 -51: =============================================================================== -51: All tests passed (6 assertions in 1 test case) -51: - 41/222 Test #50: queryTestsCatch ........................ Passed 0.03 sec +47: [12:24:54] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +47: [12:24:54] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +47: [12:24:54] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored +47: [12:24:54] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored +47: [12:24:54] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +47: =============================================================================== +47: All tests passed (1845 assertions in 63 test cases) +47: + 41/222 Test #47: chiralityTestsCatch .................... Passed 0.18 sec test 53 Start 53: smiTest1 53: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 53: Test timeout computed to be: 1500 - 42/222 Test #51: molbundleTestsCatch .................... Passed 0.04 sec +51: Randomness seeded to: 3709260737 +51: =============================================================================== +51: All tests passed (6 assertions in 1 test case) +51: + 42/222 Test #51: molbundleTestsCatch .................... Passed 0.08 sec test 54 Start 54: smiTest2 54: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 54: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 54: Test timeout computed to be: 1500 -52: Randomness seeded to: 3614021604 +52: Randomness seeded to: 3822555643 52: =============================================================================== 52: All tests passed (34 assertions in 1 test case) 52: - 43/222 Test #52: pickleTestsCatch ....................... Passed 0.04 sec + 43/222 Test #52: pickleTestsCatch ....................... Passed 0.07 sec test 55 Start 55: cxsmilesTest 55: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 55: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 55: Test timeout computed to be: 1500 -54: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -54: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -54: [03:17:29] SMILES Parse Error: syntax error while parsing: - -54: [03:17:29] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -54: [03:17:29] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -54: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -54: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -54: [03:17:29] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -54: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -54: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -54: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -54: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -54: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -54: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -54: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors - 44/222 Test #54: smiTest2 ............................... Passed 0.02 sec +54: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +54: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +54: [12:24:54] SMILES Parse Error: syntax error while parsing: - +54: [12:24:54] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +54: [12:24:54] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +54: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +54: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +54: [12:24:54] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +54: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +54: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +54: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +54: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +54: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +54: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +54: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 44/222 Test #54: smiTest2 ............................... Passed 0.04 sec test 56 Start 56: smaTest1 56: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 56: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 56: Test timeout computed to be: 1500 -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] WARNING: not removing hydrogen atom without neighbors -53: [03:17:29] Invalid chiral specification on atom 0 -53: [03:17:29] Invalid chiral specification on atom 0 -53: [03:17:29] Invalid chiral specification on atom 0 -53: [03:17:29] Invalid chiral specification on atom 0 -53: [03:17:29] Invalid chiral specification on atom 0 -53: [03:17:29] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -53: [03:17:29] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -3: dynamic RDValue:0.037281 s +3: dynamic RDValue:0.037127 s 3: deleted! -3: [03:17:29] ------------------------------------- -3: [03:17:29] Testing String Pickle Roundtrips. -3: [03:17:29] done -3: [03:17:29] ------------------------------------- -3: [03:17:29] Testing conversion of vect to string. -3: [03:17:29] done -3: [03:17:29] ------------------------------------- -3: [03:17:29] Testing returning const references. -3: [03:17:29] any cast -3: [03:17:29] done: 0.000835 300000 -3: [03:17:29] copy -3: [03:17:29] done: 0.000872 300000 -3: [03:17:29] ref -3: [03:17:29] done: 0.000834 300000 -3: [03:17:29] dict -3: [03:17:29] done: 0.003344 300000 -3: [03:17:29] ref with hasVal -3: [03:17:29] done: 0.001291 300000 -3: [03:17:29] done -3: [03:17:29] ------------------------------------- -3: [03:17:29] Testing dict update. -3: [03:17:29] done +3: [12:24:54] ------------------------------------- +3: [12:24:54] Testing String Pickle Roundtrips. +3: [12:24:54] done +3: [12:24:54] ------------------------------------- +3: [12:24:54] Testing conversion of vect to string. +3: [12:24:54] done +3: [12:24:54] ------------------------------------- +3: [12:24:54] Testing returning const references. +3: [12:24:54] any cast +3: [12:24:54] done: 0.000834 300000 +3: [12:24:54] copy +3: [12:24:54] done: 0.000833 300000 +3: [12:24:54] ref +3: [12:24:54] done: 0.000834 300000 +3: [12:24:54] dict +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +3: [12:24:54] done: 0.003439 300000 +3: [12:24:54] ref with hasVal +53: [12:24:54] WARNING: not removing hydrogen atom without neighbors +53: [12:24:54] Invalid chiral specification on atom 0 +53: [12:24:54] Invalid chiral specification on atom 0 +53: [12:24:54] Invalid chiral specification on atom 0 +53: [12:24:54] Invalid chiral specification on atom 0 +53: [12:24:54] Invalid chiral specification on atom 0 +3: [12:24:54] done: 0.001281 300000 +3: [12:24:54] done +3: [12:24:54] ------------------------------------- +3: [12:24:54] Testing dict update. +3: [12:24:54] done 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! - 45/222 Test #3: testDict ............................... Passed 1.00 sec + 45/222 Test #3: testDict ............................... Passed 2.15 sec test 57 Start 57: smiTestCatch 57: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 57: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 -53: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -56: [03:17:29] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -56: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -56: [03:17:29] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -56: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -56: [03:17:29] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -56: [03:17:29] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 46/222 Test #56: smaTest1 ............................... Passed 0.09 sec +53: [12:24:54] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +53: [12:24:54] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +26: ... +26: ---------------------------------------------------------------------- +26: Ran 12 tests in 0.794s +26: +26: OK +57: Randomness seeded to: 596818743 +57: [12:24:54] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +57: [12:24:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +57: [12:24:54] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +57: [12:24:54] SMARTS Parse Error: unclosed ring for input: 'C1C' +57: [12:24:54] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +57: [12:24:54] SMARTS Parse Error: syntax error while parsing: C)foo +57: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +57: [12:24:54] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +57: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +57: [12:24:54] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +32: [12:24:54] Maximum BFS search size exceeded. +32: This is likely due to a highly symmetric fused ring system. +57: [12:24:54] w block attempts to set wedging on bond 0 more than once. +57: [12:24:54] improperly formatted w block +57: [12:24:54] atom 3 is not associated with bond 1 in w block +57: =============================================================================== +57: All tests passed (1516 assertions in 53 test cases) +57: + 46/222 Test #57: smiTestCatch ........................... Passed 0.26 sec test 58 Start 58: nontetrahedralCatch 58: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 58: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 +53: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +56: [12:24:54] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +56: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +56: [12:24:54] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +56: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +56: [12:24:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +56: [12:24:54] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 47/222 Test #56: smaTest1 ............................... Passed 0.33 sec +test 59 + Start 59: testDepictor + +59: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor +59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor +59: Test timeout computed to be: 1500 +58: Randomness seeded to: 2689801672 +58: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 53: smi: ClC1CCCCC1 53: smi: ClC1CCCCC1 53: smi: ClC1CCCCC1Br @@ -13242,111 +13304,61 @@ 53: CaC(bC)aC 53: CbC(bC)aC 53: O.C +58: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry 53: 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 -53: [03:17:29] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -53: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -53: [03:17:29] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -53: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -53: [03:17:29] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -53: [03:17:29] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -53: [03:17:29] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [03:17:29] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [03:17:29] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [03:17:29] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [03:17:29] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [03:17:29] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: C=c1s/c2n(c1=O)CCCCCCC\N=2 -53: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -53: [03:17:29] SMILES Parse Error: extra close parentheses while parsing: C) -53: [03:17:29] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' -57: Randomness seeded to: 2650249904 -57: [03:17:29] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -57: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -57: [03:17:29] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' - 47/222 Test #53: smiTest1 ............................... Passed 0.14 sec -test 59 - Start 59: testDepictor - -59: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/testDepictor -59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor -59: Test timeout computed to be: 1500 -57: [03:17:29] SMARTS Parse Error: unclosed ring for input: 'C1C' -57: [03:17:29] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -57: [03:17:29] SMARTS Parse Error: syntax error while parsing: C)foo -57: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -57: [03:17:29] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -57: [03:17:29] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -58: Randomness seeded to: 1701827550 -58: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -57: [03:17:29] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -58: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [03:17:29] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [03:17:29] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -58: =============================================================================== -58: All tests passed (308 assertions in 9 test cases) -58: - 48/222 Test #58: nontetrahedralCatch .................... Passed 0.04 sec +53: [12:24:54] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +53: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +53: [12:24:54] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +53: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +53: [12:24:54] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +53: [12:24:54] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +58: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry + 48/222 Test #26: pyForceFieldConstraints ................ Passed 1.99 sec test 60 Start 60: depictorCatch 60: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/depictorCatch 60: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor 60: Test timeout computed to be: 1500 -26: ... -26: ---------------------------------------------------------------------- -26: Ran 12 tests in 0.566s -26: -26: OK -57: [03:17:29] w block attempts to set wedging on bond 0 more than once. -57: [03:17:29] improperly formatted w block -57: [03:17:29] atom 3 is not associated with bond 1 in w block -32: [03:17:29] Maximum BFS search size exceeded. -32: This is likely due to a highly symmetric fused ring system. -32: F/C=C/Cl -32: [H]/C(F)=C(/[H])Cl -32: F/C=C/Cl -32: F/C=C/Cl -32: C/C(F)=C(/C)Cl - 49/222 Test #32: graphmolMolOpsTest ..................... Passed 0.69 sec +58: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [12:24:54] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [12:24:54] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +58: =============================================================================== +58: All tests passed (308 assertions in 9 test cases) +58: +53: [12:24:54] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [12:24:54] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [12:24:54] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [12:24:54] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [12:24:54] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [12:24:54] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [12:24:54] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: C=c1s/c2n(c1=O)CCCCCCC\N=2 +53: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +53: [12:24:54] SMILES Parse Error: extra close parentheses while parsing: C) +53: [12:24:54] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 49/222 Test #58: nontetrahedralCatch .................... Passed 0.11 sec test 61 Start 61: pyDepictor 61: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" 61: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Depictor/Wrap 61: Test timeout computed to be: 1500 -57: =============================================================================== -57: All tests passed (1516 assertions in 53 test cases) -57: - 50/222 Test #26: pyForceFieldConstraints ................ Passed 0.90 sec - 51/222 Test #57: smiTestCatch ........................... Passed 0.17 sec + 50/222 Test #53: smiTest1 ............................... Passed 0.51 sec test 62 Start 62: testMrvToMol 62: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol 62: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MarvinParse 62: Test timeout computed to be: 1500 -test 63 - Start 63: fileParsersTest1 - -63: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -63: Test timeout computed to be: 1500 -59: [03:17:29] Warning: stereochemistry around double bond may be incorrect in depiction. -63: *************************************** -63: *************************************** -63: [03:17:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: [03:17:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 62: Using new chirality perception 62: Test 62: @@ -13376,68 +13388,24 @@ 62: 62: ProblemShort.mol 62: -62: [03:17:29] For a MultipleSgroup expansion, the matching orphaned bond was not found +62: [12:24:54] For a MultipleSgroup expansion, the matching orphaned bond was not found 62: The multiple sgroup will be ignored -63: [03:17:29] bond with order 0 found on line 7. This is not part of the MDL specification. -60: Randomness seeded to: 2482656420 +60: Randomness seeded to: 141424288 60: =============================================================================== 60: All tests passed (571 assertions in 14 test cases) 60: - 52/222 Test #59: testDepictor ........................... Passed 0.23 sec -test 64 - Start 64: testMolSupplier - -64: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -64: Test timeout computed to be: 1500 - 53/222 Test #60: depictorCatch .......................... Passed 0.21 sec -test 65 - Start 65: testGeneralFileReader - -65: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -65: Test timeout computed to be: 1500 -63: [03:17:29] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -63: [03:17:29] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -63: [03:17:29] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -64: [03:17:30] -64: ----------------------------------------- -63: generating smiles -63: 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 -63: converting back -65: [03:17:30] -65: ----------------------------------------- -65: [03:17:30] Finished: testDetermineFormat() -65: [03:17:30] ----------------------------------------- -65: -65: [03:17:30] -65: ----------------------------------------- -63: check isomorphism -64: [03:17:30] -64: -64: **** -64: Invariant Violation -64: bad prop value -64: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -64: Failed Expression: nSwaps < 2 -64: **** -64: -55: Randomness seeded to: 3047470903 -55: =============================================================================== -55: All tests passed (1902 assertions in 21 test cases) -55: - 54/222 Test #55: cxsmilesTest ........................... Passed 0.41 sec -test 66 - Start 66: testMultithreadedMolSupplier + 51/222 Test #60: depictorCatch .......................... Passed 0.30 sec +test 63 + Start 63: fileParsersTest1 -66: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -66: Test timeout computed to be: 1500 -65: [03:17:30] Finished: testSdf() -65: [03:17:30] ----------------------------------------- -65: -65: [03:17:30] -65: ----------------------------------------- +63: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +63: Test timeout computed to be: 1500 +63: *************************************** +63: *************************************** +63: [12:24:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +63: [12:24:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +63: [12:24:55] bond with order 0 found on line 7. This is not part of the MDL specification. 62: Test 62: 62: lostStereoAnd.sdf @@ -13718,10 +13686,8 @@ 62: 62: MulticenterSgroup.mrv 62: -62: [03:17:30] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -62: [03:17:30] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -66: [03:17:30] -66: ----------------------------------------- +62: [12:24:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +62: [12:24:55] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 62: Test 62: 62: GenericSgroup.mrv @@ -13754,7 +13720,7 @@ 62: 62: MarvinBadMissingMolID.mrv 62: -62: [03:17:30] +62: [12:24:55] 62: 62: **** 62: Test Assert @@ -13805,6 +13771,9 @@ 62: MarvinBadMissingSruMolID.mrv 62: 62: Expected a molID in MRV file +63: [12:24:55] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +63: [12:24:55] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +63: [12:24:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 62: Test 62: 62: MarvinBadMissingSruID.mrv @@ -13889,141 +13858,11 @@ 62: MarvinBadSupMissingAttachOrder.mrv 62: 62: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -64: [03:17:30] Finished: testMolSup() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testRandMolSup() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -65: [03:17:30] Finished: testSmi() -65: [03:17:30] ----------------------------------------- -65: -65: [03:17:30] -65: ----------------------------------------- -64: [03:17:30] Finished: testSmilesSup() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] ------------------------------------------------------ -64: [03:17:30] SMILES Parse Error: syntax error while parsing: fail -64: [03:17:30] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -64: [03:17:30] ERROR: Smiles parse error on line 3 -64: [03:17:30] ERROR: Cannot create molecule from : 'fail' -64: [03:17:30] ------------------------------------------------------ -64: [03:17:30] ------------------------------------------------------ -64: [03:17:30] >>> This may result in an infinite loop. It should finish almost immediately: -64: [03:17:30] <<< done. -64: [03:17:30] Finished: testSmilesSupFromText() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testSmilesWriter() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testSDWriter() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testSDSupplierEnding() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testSuppliersEmptyFile() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testCisTrans() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testStereoRound() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [03:17:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [03:17:30] Finished: testIssue226() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testTDTSupplier1() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testTDTSupplier2() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testTDTSupplier3() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testSDSupplierFromText() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] ERROR: Problems encountered parsing data fields -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] ERROR: Problems encountered parsing data fields -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Spurious data before the first property will be ignored -64: [03:17:30] Property will be truncated after the first blank line -64: [03:17:30] Property will be truncated after the first blank line -64: [03:17:30] Property will be truncated after the first blank line -64: [03:17:30] Finished: testSDSupplierStrLax1() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] ERROR: Problems encountered parsing data fields -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Property will be truncated after the first blank line -64: [03:17:30] Finished: testSDSupplierStrLax2() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] ERROR: Problems encountered parsing data fields -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] ERROR: Problems encountered parsing data fields -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Spurious data before the first property will be ignored -64: [03:17:30] Property will be truncated after the first blank line -64: [03:17:30] Property will be truncated after the first blank line -64: [03:17:30] Property will be truncated after the first blank line -64: [03:17:30] Finished: testSDSupplierFromTextStrLax1() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] ERROR: Problems encountered parsing data fields -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Property will be truncated after the first blank line -64: [03:17:30] Finished: testSDSupplierFromTextStrLax2() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testIssue265() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] ERROR: End of data field name not found -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Explicit valence for atom # 0 F, 2, is greater than permitted -64: [03:17:30] ERROR: Could not sanitize molecule ending on line 16 -64: [03:17:30] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -64: [03:17:30] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] ERROR: Bond line too short: 'M END' on line 18 -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Finished: testSDErrorHandling() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testIssue381() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- +63: generating smiles +63: 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 +63: converting back +59: [12:24:55] Warning: stereochemistry around double bond may be incorrect in depiction. +63: check isomorphism 62: Test 62: 62: marvin03.mrv @@ -14068,58 +13907,9 @@ 62: 62: EmptyRxn.mrv 62: -62: [03:17:30] initialization failed -64: [03:17:30] Finished: testSetStreamIndices() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testMixIterAndRandom() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: build: -64: [03:17:30] Finished: testRemoveHs() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testGetItemText() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testForwardSDSupplier() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testMissingCRSDSupplier() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testIssue3482695() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] ERROR: Cannot convert 'foo' to unsigned int on line 557 -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Finished: testIssue3525673() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testBlankLinesInProps() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testSkipLines() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testGitHub23() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testGitHub88() -64: [03:17:30] ----------------------------------------- -64: -64: [03:17:30] ----------------------------------------- +62: [12:24:55] initialization failed +32: [12:24:55] Maximum BFS search size exceeded. +32: This is likely due to a highly symmetric fused ring system. 62: Test 62: 62: RxnNoCoords.mrv @@ -14204,92 +13994,333 @@ 62: 62: Smiles1 62: - 55/222 Test #62: testMrvToMol ........................... Passed 0.27 sec + 52/222 Test #62: testMrvToMol ........................... Passed 0.56 sec +test 64 + Start 64: testMolSupplier + +64: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +64: Test timeout computed to be: 1500 +32: F/C=C/Cl +32: [H]/C(F)=C(/[H])Cl +32: F/C=C/Cl +32: F/C=C/Cl +32: C/C(F)=C(/C)Cl +64: [12:24:55] +64: ----------------------------------------- + 53/222 Test #32: graphmolMolOpsTest ..................... Passed 2.01 sec +test 65 + Start 65: testGeneralFileReader + +65: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +65: Test timeout computed to be: 1500 +64: [12:24:55] +64: +64: **** +64: Invariant Violation +64: bad prop value +64: Violation occurred on line 158 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +64: Failed Expression: nSwaps < 2 +64: **** +64: + 54/222 Test #59: testDepictor ........................... Passed 0.76 sec +test 66 + Start 66: testMultithreadedMolSupplier + +66: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +66: Test timeout computed to be: 1500 +65: [12:24:55] +65: ----------------------------------------- +65: [12:24:55] Finished: testDetermineFormat() +65: [12:24:55] ----------------------------------------- +65: +65: [12:24:55] +65: ----------------------------------------- +66: [12:24:55] +66: ----------------------------------------- +65: [12:24:55] Finished: testSdf() +65: [12:24:55] ----------------------------------------- +65: +65: [12:24:55] +65: ----------------------------------------- +65: [12:24:55] Finished: testSmi() +65: [12:24:55] ----------------------------------------- +65: +65: [12:24:55] +65: ----------------------------------------- +64: [12:24:55] Finished: testMolSup() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testRandMolSup() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testSmilesSup() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] ------------------------------------------------------ +64: [12:24:55] SMILES Parse Error: syntax error while parsing: fail +64: [12:24:55] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +64: [12:24:55] ERROR: Smiles parse error on line 3 +64: [12:24:55] ERROR: Cannot create molecule from : 'fail' +64: [12:24:55] ------------------------------------------------------ +64: [12:24:55] ------------------------------------------------------ +64: [12:24:55] >>> This may result in an infinite loop. It should finish almost immediately: +64: [12:24:55] <<< done. +64: [12:24:55] Finished: testSmilesSupFromText() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testSmilesWriter() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +55: Randomness seeded to: 1855267671 +55: =============================================================================== +55: All tests passed (1902 assertions in 21 test cases) +55: + 55/222 Test #55: cxsmilesTest ........................... Passed 1.34 sec test 67 Start 67: testMolWriter 67: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMolWriter 67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 -64: [03:17:30] Finished: testGitHub2285() -64: [03:17:30] ----------------------------------------- +64: [12:24:55] Finished: testSDWriter() +64: [12:24:55] ----------------------------------------- 64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -64: [03:17:30] ERROR: Smiles parse error on line 1 -64: [03:17:30] ERROR: Cannot create molecule from : 'c1ccccc' -64: [03:17:30] SMILES Parse Error: extra open parentheses for input: 'C(C' -64: [03:17:30] ERROR: Smiles parse error on line 3 -64: [03:17:30] ERROR: Cannot create molecule from : 'C(C' -64: [03:17:30] Explicit valence for atom # 1 C, 5, is greater than permitted -64: [03:17:30] ERROR: Could not sanitize molecule on line 5 -64: [03:17:30] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -64: [03:17:30] Explicit valence for atom # 1 F, 2, is greater than permitted -64: [03:17:30] ERROR: Could not sanitize molecule ending on line 21 -64: [03:17:30] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -64: [03:17:30] Explicit valence for atom # 1 F, 2, is greater than permitted -64: [03:17:30] ERROR: Could not sanitize molecule ending on line 21 -64: [03:17:30] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -64: [03:17:30] Explicit valence for atom # 1 F, 2, is greater than permitted -64: [03:17:30] ERROR: Could not sanitize molecule ending on line 21 -64: [03:17:30] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -64: [03:17:30] ERROR: Atom line too short: ' -9.6' on line 28 -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Explicit valence for atom # 1 F, 2, is greater than permitted -64: [03:17:30] ERROR: Could not sanitize molecule ending on line 21 -64: [03:17:30] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -64: [03:17:30] ERROR: Atom line too short: ' -9.6' on line 28 -64: [03:17:30] ERROR: moving to the beginning of the next molecule -64: [03:17:30] Finished: testGitHub2479() -64: [03:17:30] ----------------------------------------- +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testSDSupplierEnding() +64: [12:24:55] ----------------------------------------- 64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testSuppliersEmptyFile() +64: [12:24:55] ----------------------------------------- 64: -64: **** -64: Invariant Violation -64: bad chiral bond -64: Violation occurred on line 164 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -64: Failed Expression: bnd -64: **** +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testCisTrans() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testStereoRound() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [12:24:55] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [12:24:55] Finished: testIssue226() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testTDTSupplier1() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testTDTSupplier2() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testTDTSupplier3() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testSDSupplierFromText() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] ERROR: Problems encountered parsing data fields +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] ERROR: Problems encountered parsing data fields +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Spurious data before the first property will be ignored +64: [12:24:55] Property will be truncated after the first blank line +64: [12:24:55] Property will be truncated after the first blank line +64: [12:24:55] Property will be truncated after the first blank line +64: [12:24:55] Finished: testSDSupplierStrLax1() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] ERROR: Problems encountered parsing data fields +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Property will be truncated after the first blank line +64: [12:24:55] Finished: testSDSupplierStrLax2() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] ERROR: Problems encountered parsing data fields +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] ERROR: Problems encountered parsing data fields +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Spurious data before the first property will be ignored +64: [12:24:55] Property will be truncated after the first blank line +64: [12:24:55] Property will be truncated after the first blank line +64: [12:24:55] Property will be truncated after the first blank line +64: [12:24:55] Finished: testSDSupplierFromTextStrLax1() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] ERROR: Problems encountered parsing data fields +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Property will be truncated after the first blank line +64: [12:24:55] Finished: testSDSupplierFromTextStrLax2() +64: [12:24:55] ----------------------------------------- 64: -64: [03:17:30] Finished: testGitHub2881() -64: [03:17:30] ----------------------------------------- +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testIssue265() +64: [12:24:55] ----------------------------------------- 64: -64: [03:17:30] ----------------------------------------- -64: [03:17:30] Finished: testGitHub3517() -64: [03:17:30] ----------------------------------------- +64: [12:24:55] ----------------------------------------- +64: [12:24:55] ERROR: End of data field name not found +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Explicit valence for atom # 0 F, 2, is greater than permitted +64: [12:24:55] ERROR: Could not sanitize molecule ending on line 16 +64: [12:24:55] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +64: [12:24:55] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] ERROR: Bond line too short: 'M END' on line 18 +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Finished: testSDErrorHandling() +64: [12:24:55] ----------------------------------------- 64: -65: [03:17:30] Finished: testMae() -65: [03:17:30] ----------------------------------------- +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testIssue381() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +65: [12:24:55] Finished: testMae() +65: [12:24:55] ----------------------------------------- 65: -65: [03:17:30] +65: [12:24:55] 65: ----------------------------------------- -65: [03:17:30] Finished: testTdt() -65: [03:17:30] ----------------------------------------- +65: [12:24:55] Finished: testTdt() +65: [12:24:55] ----------------------------------------- 65: - 56/222 Test #64: testMolSupplier ........................ Passed 0.19 sec - 57/222 Test #65: testGeneralFileReader .................. Passed 0.18 sec + 56/222 Test #65: testGeneralFileReader .................. Passed 0.30 sec test 68 Start 68: testTplParser 68: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testTplParser 68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 68: Test timeout computed to be: 1500 +64: [12:24:55] Finished: testSetStreamIndices() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testMixIterAndRandom() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: build: +64: [12:24:55] Finished: testRemoveHs() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testGetItemText() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- + 57/222 Test #68: testTplParser .......................... Passed 0.05 sec test 69 Start 69: testMol2ToMol 69: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 69: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 - 58/222 Test #68: testTplParser .......................... Passed 0.04 sec - 59/222 Test #69: testMol2ToMol .......................... Passed 0.02 sec +64: [12:24:55] Finished: testForwardSDSupplier() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testMissingCRSDSupplier() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testIssue3482695() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] ERROR: Cannot convert 'foo' to unsigned int on line 557 +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Finished: testIssue3525673() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testBlankLinesInProps() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testSkipLines() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testGitHub23() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testGitHub88() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testGitHub2285() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +64: [12:24:55] ERROR: Smiles parse error on line 1 +64: [12:24:55] ERROR: Cannot create molecule from : 'c1ccccc' +64: [12:24:55] SMILES Parse Error: extra open parentheses for input: 'C(C' +64: [12:24:55] ERROR: Smiles parse error on line 3 +64: [12:24:55] ERROR: Cannot create molecule from : 'C(C' +64: [12:24:55] Explicit valence for atom # 1 C, 5, is greater than permitted +64: [12:24:55] ERROR: Could not sanitize molecule on line 5 +64: [12:24:55] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +64: [12:24:55] Explicit valence for atom # 1 F, 2, is greater than permitted +64: [12:24:55] ERROR: Could not sanitize molecule ending on line 21 +64: [12:24:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +64: [12:24:55] Explicit valence for atom # 1 F, 2, is greater than permitted +64: [12:24:55] ERROR: Could not sanitize molecule ending on line 21 +64: [12:24:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +64: [12:24:55] Explicit valence for atom # 1 F, 2, is greater than permitted +64: [12:24:55] ERROR: Could not sanitize molecule ending on line 21 +64: [12:24:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +64: [12:24:55] ERROR: Atom line too short: ' -9.6' on line 28 +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Explicit valence for atom # 1 F, 2, is greater than permitted +64: [12:24:55] ERROR: Could not sanitize molecule ending on line 21 +64: [12:24:55] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +64: [12:24:55] ERROR: Atom line too short: ' -9.6' on line 28 +64: [12:24:55] ERROR: moving to the beginning of the next molecule +64: [12:24:55] Finished: testGitHub2479() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] +64: +64: **** +64: Invariant Violation +64: bad chiral bond +64: Violation occurred on line 164 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +64: Failed Expression: bnd +64: **** +64: +64: [12:24:55] Finished: testGitHub2881() +64: [12:24:55] ----------------------------------------- +64: +64: [12:24:55] ----------------------------------------- +64: [12:24:55] Finished: testGitHub3517() +64: [12:24:55] ----------------------------------------- +64: + 58/222 Test #64: testMolSupplier ........................ Passed 0.50 sec test 70 Start 70: testSequence 70: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testSequence 70: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 + 59/222 Test #69: testMol2ToMol .......................... Passed 0.09 sec test 71 Start 71: testExtendedStereoParsing @@ -15280,8 +15311,8 @@ 70: CONECT 27 28 28 29 70: END 70: - 60/222 Test #70: testSequence ........................... Passed 0.07 sec - 61/222 Test #71: testExtendedStereoParsing .............. Passed 0.06 sec + 60/222 Test #70: testSequence ........................... Passed 0.14 sec + 61/222 Test #71: testExtendedStereoParsing .............. Passed 0.11 sec test 72 Start 72: fileParsersCatchTest @@ -15294,41 +15325,37 @@ 73: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists 73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 73: Test timeout computed to be: 1500 -67: [03:17:30] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -67: [03:17:30] bond with order 0 found on line 11. This is not part of the MDL specification. -67: [03:17:30] bond with order 0 found on line 16. This is not part of the MDL specification. - 62/222 Test #67: testMolWriter .......................... Passed 0.17 sec +72: Randomness seeded to: 1085143805 +72: [12:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +73: Randomness seeded to: 319661130 +73: =============================================================================== +73: All tests passed (95 assertions in 4 test cases) +73: + 62/222 Test #73: testPropertyLists ...................... Passed 0.08 sec test 74 Start 74: XYZFileParserCatchTest 74: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers 74: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -72: Randomness seeded to: 1315540641 -72: [03:17:30] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -72: [03:17:30] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -72: [03:17:30] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -72: [03:17:30] SGroup 1 is invalid and will be ignored -74: Randomness seeded to: 3871976625 -74: =============================================================================== -74: All tests passed (100 assertions in 2 test cases) -74: -72: [03:17:30] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -72: [03:17:30] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -72: [03:17:30] SGroup 1 is invalid and will be ignored -72: [03:17:30] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -72: [03:17:30] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -72: [03:17:30] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -72: [03:17:30] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -72: [03:17:30] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -72: [03:17:30] SGroup 1 is invalid and will be ignored -72: [03:17:30] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -72: [03:17:30] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -72: [03:17:30] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -72: [03:17:30] SGroup 1 is invalid and will be ignored -72: [03:17:30] SGroup 3 referenced on line 40 not found. -72: [03:17:30] +72: [12:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +72: [12:24:56] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +72: [12:24:56] SGroup 1 is invalid and will be ignored +72: [12:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +72: [12:24:56] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +72: [12:24:56] SGroup 1 is invalid and will be ignored +72: [12:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +72: [12:24:56] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +72: [12:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +72: [12:24:56] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +72: [12:24:56] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +72: [12:24:56] SGroup 1 is invalid and will be ignored +72: [12:24:56] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +72: [12:24:56] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +72: [12:24:56] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +72: [12:24:56] SGroup 1 is invalid and will be ignored +72: [12:24:56] SGroup 3 referenced on line 40 not found. +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15337,8 +15364,8 @@ 72: Failed Expression: !d_bonds.empty() 72: **** 72: -72: [03:17:30] SGroup 3 referenced on line 40 not found. -72: [03:17:30] +72: [12:24:56] SGroup 3 referenced on line 40 not found. +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15347,13 +15374,13 @@ 72: Failed Expression: !d_bonds.empty() 72: **** 72: -72: [03:17:30] no bonds -72: [03:17:30] SGroup 1 is invalid and will be ignored -72: [03:17:30] SGroup line too short: 'M SBV 1 6' on line 42 -72: [03:17:30] SGroup 1 is invalid and will be ignored -72: [03:17:30] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -72: [03:17:30] SGroup 2 is invalid and will be ignored -72: [03:17:30] +72: [12:24:56] no bonds +72: [12:24:56] SGroup 1 is invalid and will be ignored +72: [12:24:56] SGroup line too short: 'M SBV 1 6' on line 42 +72: [12:24:56] SGroup 1 is invalid and will be ignored +72: [12:24:56] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +72: [12:24:56] SGroup 2 is invalid and will be ignored +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15362,7 +15389,7 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15371,8 +15398,8 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [03:17:30] bookmark not found -72: [03:17:30] +72: [12:24:56] bookmark not found +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15381,9 +15408,9 @@ 72: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 72: **** 72: -72: [03:17:30] bond is not part of the SubstanceGroup -72: [03:17:30] SGroup 2 is invalid and will be ignored -72: [03:17:30] +72: [12:24:56] bond is not part of the SubstanceGroup +72: [12:24:56] SGroup 2 is invalid and will be ignored +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15392,7 +15419,7 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15401,11 +15428,11 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [03:17:30] bookmark not found -72: [03:17:30] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -72: [03:17:30] SGroup 2 is invalid and will be ignored -72: [03:17:30] WARNING: final character of V3000 array is not ')' -72: [03:17:30] +72: [12:24:56] bookmark not found +72: [12:24:56] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +72: [12:24:56] SGroup 2 is invalid and will be ignored +72: [12:24:56] WARNING: final character of V3000 array is not ')' +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15414,8 +15441,8 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [03:17:30] WARNING: final character of V3000 array is not ')' -72: [03:17:30] +72: [12:24:56] WARNING: final character of V3000 array is not ')' +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15424,10 +15451,10 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [03:17:30] bookmark not found -72: [03:17:30] SGroup 1 is invalid and will be ignored -72: [03:17:30] WARNING: final character of V3000 array is not ')' -72: [03:17:30] +72: [12:24:56] bookmark not found +72: [12:24:56] SGroup 1 is invalid and will be ignored +72: [12:24:56] WARNING: final character of V3000 array is not ')' +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15436,8 +15463,8 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [03:17:30] WARNING: final character of V3000 array is not ')' -72: [03:17:30] +72: [12:24:56] WARNING: final character of V3000 array is not ')' +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15446,9 +15473,9 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [03:17:30] bookmark not found -72: [03:17:30] SGroup 1 is invalid and will be ignored -72: [03:17:30] +72: [12:24:56] bookmark not found +72: [12:24:56] SGroup 1 is invalid and will be ignored +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15457,7 +15484,7 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15466,27 +15493,9 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [03:17:30] bookmark not found -72: [03:17:30] SGroup 2 is invalid and will be ignored -73: Randomness seeded to: 3605016422 -73: =============================================================================== -73: All tests passed (95 assertions in 4 test cases) -73: - 63/222 Test #73: testPropertyLists ...................... Passed 0.05 sec - 64/222 Test #74: XYZFileParserCatchTest ................. Passed 0.04 sec -test 75 - Start 75: cdxmlParserCatchTest - -75: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -75: Test timeout computed to be: 1500 -test 76 - Start 76: molfileStereoCatchTest - -76: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -72: [03:17:30] +72: [12:24:56] bookmark not found +72: [12:24:56] SGroup 2 is invalid and will be ignored +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15495,7 +15504,7 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15504,14 +15513,17 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [03:17:30] bookmark not found -72: [03:17:30] SGroup 2 is invalid and will be ignored -72: [03:17:30] Explicit valence for atom # 2 O, 3, is greater than permitted -72: [03:17:30] Explicit valence for atom # 1 O, 3, is greater than permitted -72: [03:17:30] Explicit valence for atom # 1 C, 5, is greater than permitted -72: [03:17:30] sanitize [03:17:30] UNK: [03:17:30] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -72: [03:17:30] skipping block at line 7: 'BEGIN ATOM' -72: [03:17:30] +72: [12:24:56] bookmark not found +72: [12:24:56] SGroup 2 is invalid and will be ignored +72: [12:24:56] Explicit valence for atom # 2 O, 3, is greater than permitted +72: [12:24:56] Explicit valence for atom # 1 O, 3, is greater than permitted +72: [12:24:56] Explicit valence for atom # 1 C, 5, is greater than permitted +67: [12:24:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +72: [12:24:56] sanitize [12:24:56] UNK: [12:24:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +67: [12:24:56] bond with order 0 found on line 11. This is not part of the MDL specification. +67: [12:24:56] bond with order 0 found on line 16. This is not part of the MDL specification. +72: [12:24:56] skipping block at line 7: 'BEGIN ATOM' +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15520,7 +15532,7 @@ 72: Failed Expression: dp_inStream 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15529,7 +15541,7 @@ 72: Failed Expression: dp_inStream 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15538,7 +15550,7 @@ 72: Failed Expression: dp_inStream 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15547,7 +15559,7 @@ 72: Failed Expression: dp_inStream 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15556,9 +15568,20 @@ 72: Failed Expression: dp_sInStream != nullptr 72: **** 72: -72: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 21 -72: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 20 -72: [03:17:30] + 63/222 Test #67: testMolWriter .......................... Passed 0.51 sec +test 75 + Start 75: cdxmlParserCatchTest + +75: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +75: Test timeout computed to be: 1500 +74: Randomness seeded to: 4280310467 +74: =============================================================================== +74: All tests passed (100 assertions in 2 test cases) +74: +72: [12:24:56] Found a SCD/SED line with missing/empty SDT specification at line 21 +72: [12:24:56] Found a SCD/SED line with missing/empty SDT specification at line 20 +72: [12:24:56] 72: 72: **** 72: Post-condition Violation @@ -15567,20 +15590,13 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [03:17:30] BEGIN SGROUP line not found on line 14 -72: [03:17:30] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -72: [03:17:30] END SGROUP line not found on line 14 -72: [03:17:30] END SGROUP line not found on line 14 -75: Randomness seeded to: 2634635978 -75: [03:17:30] Invalid or missing fragment id from CDXML fragment, assigning new one... -75: [03:17:30] Explicit valence for atom # 3 N, 4, is greater than permitted -75: [03:17:30] CDXMLParser: failed sanitizing skipping fragment 32 -75: [03:17:30] Bad bond in CDXML skipping fragment 58... -75: [03:17:30] Invalid or missing fragment id from CDXML fragment, assigning new one... -75: [03:17:30] Bad bond in CDXML skipping fragment 58... -72: [03:17:30] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -72: [03:17:30] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -72: [03:17:30] +72: [12:24:56] BEGIN SGROUP line not found on line 14 +72: [12:24:56] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +72: [12:24:56] END SGROUP line not found on line 14 +72: [12:24:56] END SGROUP line not found on line 14 +72: [12:24:56] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +72: [12:24:56] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +72: [12:24:56] 72: 72: **** 72: Range Error @@ -15589,24 +15605,31 @@ 72: Failed Expression: 99 < 9 72: **** 72: -72: [03:17:30] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -72: [03:17:30] Multiple ATTCHPT values for atom 2 on line 9 -72: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 12 -72: [03:17:30] SMARTS Parse Error: syntax error while parsing: [#6;R -72: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -72: [03:17:30] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -72: [03:17:30] Skipping empty SMARTS value for SMARTSQ. -72: [03:17:30] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -72: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 12 -72: [03:17:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -72: [03:17:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:17:30] WARNING: Skipping property bar because the value includes an illegal blank line -72: [03:17:30] WARNING: Skipping property baz because the value includes an illegal blank line -72: [03:17:30] WARNING: Skipping property bletch +72: [12:24:56] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +72: [12:24:56] Multiple ATTCHPT values for atom 2 on line 9 +72: [12:24:56] Found a SCD/SED line with missing/empty SDT specification at line 12 +72: [12:24:56] SMARTS Parse Error: syntax error while parsing: [#6;R +72: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +72: [12:24:56] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +72: [12:24:56] Skipping empty SMARTS value for SMARTSQ. +72: [12:24:56] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +72: [12:24:56] Found a SCD/SED line with missing/empty SDT specification at line 12 +72: [12:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 + 64/222 Test #74: XYZFileParserCatchTest ................. Passed 0.10 sec +test 76 + Start 76: molfileStereoCatchTest + +76: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +72: [12:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [12:24:56] WARNING: Skipping property bar because the value includes an illegal blank line +72: [12:24:56] WARNING: Skipping property baz because the value includes an illegal blank line +72: [12:24:56] WARNING: Skipping property bletch 72: nope because the name includes a newline -72: [03:17:30] WARNING: Skipping property bletch +72: [12:24:56] WARNING: Skipping property bletch 72: nope2 because the name includes a newline -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Post-condition Violation @@ -15615,7 +15638,7 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Post-condition Violation @@ -15624,7 +15647,7 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Post-condition Violation @@ -15633,7 +15656,7 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Post-condition Violation @@ -15642,36 +15665,8 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [03:17:30] atom 3 has a negative isotope value. line: 15 -76: Randomness seeded to: 3831390967 -76: [03:17:30] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -76: [03:17:30] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -76: [03:17:30] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -76: [03:17:30] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -76: [03:17:30] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored -76: =============================================================================== -76: All tests passed (142 assertions in 6 test cases) -76: - 65/222 Test #76: molfileStereoCatchTest ................. Passed 0.05 sec -test 77 - Start 77: connectTheDotsTest - -77: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] WARNING: not removing hydrogen atom without neighbors -75: [03:17:30] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. -25: All 191 tests passed -72: [03:17:30] +72: [12:24:56] atom 3 has a negative isotope value. line: 15 +72: [12:24:56] 72: 72: **** 72: Invariant Violation @@ -15680,7 +15675,7 @@ 72: Failed Expression: nSwaps < 2 72: **** 72: -72: [03:17:30] +72: [12:24:56] 72: 72: **** 72: Pre-condition Violation @@ -15689,19 +15684,74 @@ 72: Failed Expression: dp_sInStream 72: **** 72: -75: [03:17:30] Incomplete atom labelling, cannot make bond -75: [03:17:30] Incomplete atom labelling, cannot make bond -77: Randomness seeded to: 1206950219 +75: Randomness seeded to: 3057752620 +75: [12:24:56] Invalid or missing fragment id from CDXML fragment, assigning new one... +75: [12:24:56] Explicit valence for atom # 3 N, 4, is greater than permitted +75: [12:24:56] CDXMLParser: failed sanitizing skipping fragment 32 +75: [12:24:56] Bad bond in CDXML skipping fragment 58... +75: [12:24:56] Invalid or missing fragment id from CDXML fragment, assigning new one... +75: [12:24:56] Bad bond in CDXML skipping fragment 58... +76: Randomness seeded to: 1857474843 +76: [12:24:56] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [12:24:56] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [12:24:56] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [12:24:56] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [12:24:56] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored +76: =============================================================================== +76: All tests passed (142 assertions in 6 test cases) +76: +61: ..............[12:24:56] SMILES Parse Error: syntax error while parsing: invalidsmiles +61: [12:24:56] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' + 65/222 Test #76: molfileStereoCatchTest ................. Passed 0.12 sec +test 77 + Start 77: connectTheDotsTest + +77: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] WARNING: not removing hydrogen atom without neighbors +75: [12:24:56] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. +72: [12:24:56] ERROR: molecules without atoms cannot be exported to Maestro files. +72: [12:24:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +72: [12:24:56] ERROR: the mol cannot be kekulized, and will not be written to the output file. +72: [12:24:56] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +75: [12:24:56] Incomplete atom labelling, cannot make bond +75: [12:24:56] Incomplete atom labelling, cannot make bond +77: Randomness seeded to: 2064011142 77: =============================================================================== 77: All tests passed (8 assertions in 1 test case) 77: - 66/222 Test #77: connectTheDotsTest ..................... Passed 0.04 sec +72: [12:24:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +72: [12:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [12:24:56] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +72: [12:24:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: =============================================================================== +72: All tests passed (1311 assertions in 87 test cases) +72: + 66/222 Test #72: fileParsersCatchTest ................... Passed 0.41 sec test 78 Start 78: testSubstructMatch 78: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch 78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct 78: Test timeout computed to be: 1500 + 67/222 Test #77: connectTheDotsTest ..................... Passed 0.09 sec +test 79 + Start 79: substructTestCatch + +79: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct +79: Test timeout computed to be: 1500 +75: [12:24:56] Incomplete atom labelling, cannot make bond 78: ----------------- Test 1 78: Done 78: @@ -15726,50 +15776,34 @@ 78: ----------------- Testing serial numbers on recursive queries 78: Done 78: -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test multithreading +78: [12:24:56] ------------------------------------- +78: [12:24:56] Test multithreading 78: reading molecules -75: [03:17:30] Incomplete atom labelling, cannot make bond -75: [03:17:30] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -75: [03:17:30] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -75: [03:17:30] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -75: [03:17:30] Failed to parse XML fragment 5 node: b attribute: Order: 5 +75: [12:24:56] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +75: [12:24:56] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +75: [12:24:56] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +75: [12:24:56] Failed to parse XML fragment 5 node: b attribute: Order: 5 75: =============================================================================== 75: All tests passed (252 assertions in 4 test cases) 75: - 67/222 Test #75: cdxmlParserCatchTest ................... Passed 0.13 sec -test 79 - Start 79: substructTestCatch + 68/222 Test #75: cdxmlParserCatchTest ................... Passed 0.29 sec +test 80 + Start 80: testGenericGroups -79: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Substruct -79: Test timeout computed to be: 1500 +80: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups +80: Test timeout computed to be: 1500 78: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 78: processing 78: launch :0 78: launch :1 78: launch :2 78: launch :3 -72: [03:17:30] ERROR: molecules without atoms cannot be exported to Maestro files. -72: [03:17:30] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -72: [03:17:30] ERROR: the mol cannot be kekulized, and will not be written to the output file. -72: [03:17:30] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -72: [03:17:30] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -72: [03:17:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [03:17:30] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -72: [03:17:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: =============================================================================== -72: All tests passed (1311 assertions in 87 test cases) -72: -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... - 68/222 Test #72: fileParsersCatchTest ................... Passed 0.22 sec -test 80 - Start 80: testGenericGroups - -80: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GenericGroups -80: Test timeout computed to be: 1500 +61: ..... +61: ---------------------------------------------------------------------- +61: Ran 19 tests in 0.969s +61: +61: OK 78: done 78: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 78: processing2 @@ -15777,6 +15811,13 @@ 78: launch2 :1 78: launch2 :2 78: launch2 :3 + 69/222 Test #61: pyDepictor ............................. Passed 2.04 sec +test 81 + Start 81: testReaction + +81: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction +81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions +81: Test timeout computed to be: 1500 78: done 78: preprocessing 3 78: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 @@ -15785,48 +15826,196 @@ 78: launch3 :1 78: launch3 :2 78: launch3 :3 -61: ..............[03:17:30] SMILES Parse Error: syntax error while parsing: invalidsmiles -61: [03:17:30] SMILES Parse Error: Failed parsing SMILES 'invalidsmiles' for input: 'invalidsmiles' -79: Randomness seeded to: 2693638619 -79: =============================================================================== -79: All tests passed (143 assertions in 7 test cases) -79: - 69/222 Test #79: substructTestCatch ..................... Passed 0.27 sec -test 81 - Start 81: testReaction - -81: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReaction -81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions -81: Test timeout computed to be: 1500 +81: smi: O=C1CNC(=O)CN1 +81: 1: O=C1CNC(=O)CN1 +81: 2: COOC +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +81: [12:24:56] 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]' +81: O=C1CNC(=O)CN1 +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] mapped atoms in the reactants were not mapped in the products. +81: unmapped numbers are: 4 +81: [12:24:56] atom 0 in product 0 has multiple charge specifications. +81: mass: 15.0001 +81: Oc1ccccn1 +81: Oc1ccc[nH]1 +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +81: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: ([C:2] +81: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +81: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: [C:2]) +81: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +81: [12:24:56] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +81: [12:24:56] 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]' +81: [12:24:56] reactant 2 has no mapped atoms. +81: [12:24:56] >> Atoms within one molecule have different RXN roles. +81: [12:24:56] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +81: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: ([C:2] +81: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +81: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +81: [12:24:56] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +81: [12:24:56] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +81: [12:24:56] reactant 0 has no mapped atoms. +81: [12:24:56] reactant 1 has no mapped atoms. +81: [12:24:56] reactant 3 has no mapped atoms. +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 3 found multiple times. +81: [12:24:56] product atom-mapping number 4 found multiple times. +81: [12:24:56] product atom-mapping number 5 found multiple times. +81: [12:24:56] product atom-mapping number 6 found multiple times. +81: [12:24:56] product atom-mapping number 7 found multiple times. +81: [12:24:56] product atom-mapping number 8 found multiple times. +81: [12:24:56] product atom-mapping number 12 found multiple times. +81: [12:24:56] product atom-mapping number 9 found multiple times. +81: [12:24:56] product atom-mapping number 10 found multiple times. +81: [12:24:56] product atom-mapping number 11 found multiple times. +81: [12:24:56] reactant 0 has no mapped atoms. +81: [12:24:56] reactant 1 has no mapped atoms. +81: [12:24:56] reactant 3 has no mapped atoms. +81: [12:24:56] reactant atom-mapping number 19 found multiple times. +81: [12:24:56] reactant atom-mapping number 25 found multiple times. +81: [12:24:56] reactant atom-mapping number 20 found multiple times. +81: [12:24:56] reactant atom-mapping number 21 found multiple times. +81: [12:24:56] reactant atom-mapping number 22 found multiple times. +81: [12:24:56] reactant atom-mapping number 23 found multiple times. +81: [12:24:56] reactant atom-mapping number 24 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +81: [12:24:56] product atom-mapping number 5 found multiple times. +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 3 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 4 found multiple times. +81: [12:24:56] product atom-mapping number 5 found multiple times. +81: [12:24:56] product atom-mapping number 2 found multiple times. +81: [12:24:56] product atom-mapping number 3 found multiple times. +81: [12:24:56] product atom-mapping number 1 found multiple times. +81: [12:24:56] product atom-mapping number 4 found multiple times. +81: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +81: [12:24:57] product atom-mapping number 5 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: [12:24:57] product atom-mapping number 5 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: F[C@@](Cl)(Br)O[C@](F)(Cl)Br +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: F[C@](Cl)(Br)O[C@](F)(Cl)Br +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 4 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] mapped atoms in the reactants were not mapped in the products. +81: unmapped numbers are: 4 +81: [12:24:57] product atom-mapping number 3 found multiple times. +81: [12:24:57] product atom-mapping number 2 found multiple times. +81: [12:24:57] product atom-mapping number 1 found multiple times. +81: [12:24:57] mapped atoms in the reactants were not mapped in the products. +81: unmapped numbers are: 4 +81: [12:24:57] product atom-mapping number 6 not found in reactants. +81: [12:24:57] product atom-mapping number 7 not found in reactants. +81: [12:24:57] product atom-mapping number 8 not found in reactants. +81: [12:24:57] product atom-mapping number 7 not found in reactants. +81: [12:24:57] product atom-mapping number 8 not found in reactants. +81: [12:24:57] product atom-mapping number 9 not found in reactants. +81: [12:24:57] product atom-mapping number 10 not found in reactants. +81: [12:24:57] mapped atoms in the reactants were not mapped in the products. +81: unmapped numbers are: 6 +81: [12:24:57] product atom-mapping number 7 not found in reactants. +81: [12:24:57] product atom-mapping number 8 not found in reactants. +81: [12:24:57] product atom-mapping number 9 not found in reactants. +81: [12:24:57] product atom-mapping number 10 not found in reactants. +81: [12:24:57] mapped atoms in the reactants were not mapped in the products. +81: unmapped numbers are: 6 +81: 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] +81: 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] 78: done -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test GitHub issue 15 -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test GitHub issue 409 -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test chiral matching -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test dative-bond matching -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test cis/trans matching -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test cis/trans matching part 2 -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -78: [03:17:30] done -78: [03:17:30] ------------------------------------- -78: [03:17:30] Testing matching E/Z against Cis/Trans stereo bonds -78: [03:17:30] +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test GitHub issue 15 +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test GitHub issue 409 +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test chiral matching +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test dative-bond matching +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test cis/trans matching +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test cis/trans matching part 2 +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +81: [12:24:57] mapped atoms in the reactants were not mapped in the products. +81: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 +78: [12:24:57] done +78: [12:24:57] ------------------------------------- +78: [12:24:57] Testing matching E/Z against Cis/Trans stereo bonds +78: [12:24:57] 78: 78: **** 78: Pre-condition Violation @@ -15835,7 +16024,7 @@ 78: Failed Expression: !matches.empty() 78: **** 78: -78: [03:17:30] +78: [12:24:57] 78: 78: **** 78: Pre-condition Violation @@ -15844,329 +16033,220 @@ 78: Failed Expression: !matches.empty() 78: **** 78: -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test substructure matching with a pathological case for symmetric SSSR -78: [03:17:30] ------------------------------------- -78: [03:17:30] Test isAtomTerminalRGroupOrQueryHydrogen - 70/222 Test #78: testSubstructMatch ..................... Passed 0.35 sec +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test substructure matching with a pathological case for symmetric SSSR +78: [12:24:57] ------------------------------------- +78: [12:24:57] Test isAtomTerminalRGroupOrQueryHydrogen + 70/222 Test #78: testSubstructMatch ..................... Passed 0.68 sec test 82 Start 82: testReactionFingerprints 82: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 82: Test timeout computed to be: 1500 -81: smi: O=C1CNC(=O)CN1 -81: 1: O=C1CNC(=O)CN1 -81: 2: COOC -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -81: [03:17:30] 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]' -82: [03:17:30] ------------------------------------- -82: [03:17:30] Test Reaction StructuralFingerprint -81: O=C1CNC(=O)CN1 -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] mapped atoms in the reactants were not mapped in the products. -81: unmapped numbers are: 4 -81: [03:17:30] atom 0 in product 0 has multiple charge specifications. -81: mass: 15.0001 -81: Oc1ccccn1 -81: Oc1ccc[nH]1 -82: [03:17:30] ------------------------------------- -82: [03:17:30] Test Reaction DifferenceFingerprint -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -81: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: ([C:2] -81: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -81: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: [C:2]) -81: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -81: [03:17:30] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -81: [03:17:30] 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]' -81: [03:17:30] reactant 2 has no mapped atoms. -81: [03:17:30] >> Atoms within one molecule have different RXN roles. -81: [03:17:30] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -81: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: ([C:2] -81: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -81: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -81: [03:17:30] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -81: [03:17:30] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -80: Randomness seeded to: 1158126865 +81: [12:24:57] product atom-mapping number 17 not found in reactants. +81: [12:24:57] product atom-mapping number 18 not found in reactants. +81: [12:24:57] mapped atoms in the reactants were not mapped in the products. +81: unmapped numbers are: 12 +80: Randomness seeded to: 2544255916 80: =============================================================================== 80: All tests passed (9408 assertions in 38 test cases) 80: - 71/222 Test #82: testReactionFingerprints ............... Passed 0.06 sec + 71/222 Test #80: testGenericGroups ...................... Passed 0.65 sec test 83 Start 83: testEnumeration 83: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 83: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 83: Test timeout computed to be: 1500 -81: [03:17:30] reactant 0 has no mapped atoms. -81: [03:17:30] reactant 1 has no mapped atoms. -81: [03:17:30] reactant 3 has no mapped atoms. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 5 found multiple times. -81: [03:17:30] product atom-mapping number 6 found multiple times. -81: [03:17:30] product atom-mapping number 7 found multiple times. -81: [03:17:30] product atom-mapping number 8 found multiple times. -81: [03:17:30] product atom-mapping number 12 found multiple times. -81: [03:17:30] product atom-mapping number 9 found multiple times. -81: [03:17:30] product atom-mapping number 10 found multiple times. -81: [03:17:30] product atom-mapping number 11 found multiple times. -81: [03:17:30] reactant 0 has no mapped atoms. -81: [03:17:30] reactant 1 has no mapped atoms. -81: [03:17:30] reactant 3 has no mapped atoms. -81: [03:17:30] reactant atom-mapping number 19 found multiple times. -81: [03:17:30] reactant atom-mapping number 25 found multiple times. -81: [03:17:30] reactant atom-mapping number 20 found multiple times. -81: [03:17:30] reactant atom-mapping number 21 found multiple times. -81: [03:17:30] reactant atom-mapping number 22 found multiple times. -81: [03:17:30] reactant atom-mapping number 23 found multiple times. -81: [03:17:30] reactant atom-mapping number 24 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -81: [03:17:30] product atom-mapping number 5 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 5 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -81: [03:17:30] product atom-mapping number 5 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 5 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: F[C@](Cl)(Br)O[C@](F)(Cl)Br -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 4 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] mapped atoms in the reactants were not mapped in the products. -81: unmapped numbers are: 4 -81: [03:17:30] product atom-mapping number 3 found multiple times. -81: [03:17:30] product atom-mapping number 2 found multiple times. -81: [03:17:30] product atom-mapping number 1 found multiple times. -81: [03:17:30] mapped atoms in the reactants were not mapped in the products. -81: unmapped numbers are: 4 -81: [03:17:30] product atom-mapping number 6 not found in reactants. -81: [03:17:30] product atom-mapping number 7 not found in reactants. -81: [03:17:30] product atom-mapping number 8 not found in reactants. -81: [03:17:30] product atom-mapping number 7 not found in reactants. -81: [03:17:30] product atom-mapping number 8 not found in reactants. -81: [03:17:30] product atom-mapping number 9 not found in reactants. -81: [03:17:30] product atom-mapping number 10 not found in reactants. -81: [03:17:30] mapped atoms in the reactants were not mapped in the products. -81: unmapped numbers are: 6 -81: [03:17:30] product atom-mapping number 7 not found in reactants. -81: [03:17:30] product atom-mapping number 8 not found in reactants. -81: [03:17:30] product atom-mapping number 9 not found in reactants. -81: [03:17:30] product atom-mapping number 10 not found in reactants. -81: [03:17:30] mapped atoms in the reactants were not mapped in the products. -81: unmapped numbers are: 6 -81: 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] -81: 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] - 72/222 Test #80: testGenericGroups ...................... Passed 0.37 sec +82: [12:24:57] ------------------------------------- +82: [12:24:57] Test Reaction StructuralFingerprint +25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +63: [12:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [12:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [12:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [12:24:57] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [12:24:57] deprecated group abbreviation ignored on line 24 +63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +63: [12:24:57] +63: +63: **** +63: Post-condition Violation +63: Element 'Mv' not found +63: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +63: Failed Expression: anum > -1 +63: **** +63: +82: [12:24:57] ------------------------------------- +82: [12:24:57] Test Reaction DifferenceFingerprint + 72/222 Test #82: testReactionFingerprints ............... Passed 0.13 sec test 84 Start 84: rxnTestCatch 84: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 84: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions 84: Test timeout computed to be: 1500 -81: [03:17:30] mapped atoms in the reactants were not mapped in the products. -81: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -81: [03:17:30] product atom-mapping number 17 not found in reactants. -81: [03:17:30] product atom-mapping number 18 not found in reactants. -81: [03:17:30] mapped atoms in the reactants were not mapped in the products. -81: unmapped numbers are: 12 -61: ..... -61: ---------------------------------------------------------------------- -61: Ran 19 tests in 0.660s -61: -61: OK -84: Randomness seeded to: 1521051774 -84: [03:17:30] atom 0 in product 0 has multiple charge specifications. -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 34 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 36 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 38 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 40 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 42 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 87 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 89 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 91 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 93 -84: [03:17:30] Found a SCD/SED line with missing/empty SDT specification at line 95 -84: [03:17:30] mapped atoms in the reactants were not mapped in the products. -84: unmapped numbers are: 2 -84: [03:17:30] mapped atoms in the reactants were not mapped in the products. -84: unmapped numbers are: 2 -84: [03:17:30] SMARTS Parse Error: unclosed ring for input: 'CC1' -84: [03:17:30] SMILES Parse Error: unclosed ring for input: 'CC1' -84: [03:17:30] mapped atoms in the reactants were not mapped in the products. -84: unmapped numbers are: 2 -84: [03:17:30] product atom-mapping number 2 not found in reactants. -84: [03:17:30] mapped atoms in the reactants were not mapped in the products. -84: unmapped numbers are: 2 -84: [03:17:30] product atom-mapping number 2 not found in reactants. -84: [03:17:30] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -84: =============================================================================== -84: All tests passed (568 assertions in 20 test cases) -84: - 73/222 Test #84: rxnTestCatch ........................... Passed 0.11 sec +81: [12:24:57] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +81: [12:24:57] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +81: +81: [12:24:57] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +81: ------------- +81: CCOc1ccccc1 +79: Randomness seeded to: 3184599815 +79: =============================================================================== +79: All tests passed (143 assertions in 7 test cases) +79: + 73/222 Test #79: substructTestCatch ..................... Passed 0.82 sec test 85 Start 85: pyChemReactions 85: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 85: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 85: Test timeout computed to be: 1500 +25: All 191 tests passed +84: Randomness seeded to: 56677131 +84: [12:24:57] atom 0 in product 0 has multiple charge specifications. +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 34 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 36 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 38 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 40 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 42 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 87 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 89 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 91 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 93 +84: [12:24:57] Found a SCD/SED line with missing/empty SDT specification at line 95 +84: [12:24:57] mapped atoms in the reactants were not mapped in the products. +84: unmapped numbers are: 2 +84: [12:24:57] mapped atoms in the reactants were not mapped in the products. +84: unmapped numbers are: 2 +84: [12:24:57] SMARTS Parse Error: unclosed ring for input: 'CC1' +84: [12:24:57] SMILES Parse Error: unclosed ring for input: 'CC1' +84: [12:24:57] mapped atoms in the reactants were not mapped in the products. +84: unmapped numbers are: 2 +84: [12:24:57] product atom-mapping number 2 not found in reactants. +84: [12:24:57] mapped atoms in the reactants were not mapped in the products. +84: unmapped numbers are: 2 +84: [12:24:57] product atom-mapping number 2 not found in reactants. 83: 30000000 30000000 -81: [03:17:31] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -81: [03:17:31] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -81: -81: [03:17:31] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -81: ------------- -81: CCOc1ccccc1 - 74/222 Test #61: pyDepictor ............................. Passed 1.22 sec +84: [12:24:57] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +84: =============================================================================== +84: All tests passed (568 assertions in 20 test cases) +84: +81: [12:24:57] reactant 0 has no mapped atoms. +81: [12:24:57] product 0 has no mapped atoms. +81: [12:24:57] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 74/222 Test #84: rxnTestCatch ........................... Passed 0.28 sec test 86 Start 86: pyChemReactionEnumerations 86: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 86: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 86: Test timeout computed to be: 1500 -81: [03:17:31] reactant 0 has no mapped atoms. -81: [03:17:31] product 0 has no mapped atoms. -81: [03:17:31] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. - 75/222 Test #81: testReaction ........................... Passed 0.39 sec + 75/222 Test #81: testReaction ........................... Passed 0.70 sec test 87 Start 87: pyChemReactionSanitize 87: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 87: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemReactions/Wrap 87: Test timeout computed to be: 1500 -63: [03:17:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [03:17:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [03:17:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [03:17:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [03:17:31] deprecated group abbreviation ignored on line 24 -63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -63: [03:17:31] -63: -63: **** -63: Post-condition Violation -63: Element 'Mv' not found -63: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -63: Failed Expression: anum > -1 -63: **** -63: -87: .[03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: .[03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +85: [12:24:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +85: [12:24:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +85: .[12:24:58] +85: +85: **** +85: Pre-condition Violation +85: getNumImplicitHs() called without preceding call to calcImplicitValence() +85: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp +85: Failed Expression: d_implicitValence > -1 +85: **** +85: +85: [12:24:58] +85: +85: **** +85: Pre-condition Violation +85: getNumImplicitHs() called without preceding call to calcImplicitValence() +85: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp +85: Failed Expression: d_implicitValence > -1 +85: **** +85: +85: .......[12:24:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +85: [12:24:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +85: [12:24:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +85: [12:24:58] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) +85: .[12:24:58] product atom-mapping number 1 found multiple times. +85: [12:24:58] product atom-mapping number 1 found multiple times. +86: [12:24:58] == testCartesianProduct +85: ................[12:24:58] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 3 +85: [12:24:58] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 3 +85: .[12:24:58] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 3 +85: ..[12:24:58] reactant 2 has no mapped atoms. +85: [12:24:58] reactant 2 has no mapped atoms. +85: [12:24:58] product 1 has no mapped atoms. +85: ........[12:24:58] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q +85: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' +85: [12:24:58] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q +85: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' +85: .[12:24:58] reactant atom-mapping number 1 found multiple times. +85: [12:24:58] product atom-mapping number 2 not found in reactants. +85: [12:24:58] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 4 +85: [12:24:58] product atom-mapping number 5 not found in reactants. +86: .[12:24:58] == testEnumerateLibrary +86: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> +86: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) +86: ResourceWarning: Enable tracemalloc to get the object allocation traceback +87: .[12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: .[12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. 87: () 87: ******************************************** 87: $RXN @@ -16480,16 +16560,16 @@ 87: M END 87: 87: ******************************************** -87: [03:17:31] reactant 0 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] product 0 has no mapped atoms. -87: [03:17:31] Could not find RLabel mapping for atom: 0 in template: 1 -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. -87: [03:17:31] reactant 1 has no mapped atoms. +87: [12:24:58] reactant 0 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] product 0 has no mapped atoms. +87: [12:24:58] Could not find RLabel mapping for atom: 0 in template: 1 +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. +87: [12:24:58] reactant 1 has no mapped atoms. 87: .. 87: ---------------------------------------------------------------------- -87: Ran 4 tests in 0.013s +87: Ran 4 tests in 0.053s 87: 87: OK 87: $RXN @@ -16588,48 +16668,68 @@ 87: M END 87: 87: $RXN Failed -85: [03:17:31] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -86: [03:17:31] == testCartesianProduct -85: [03:17:31] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -85: .[03:17:31] -85: -85: **** -85: Pre-condition Violation -85: getNumImplicitHs() called without preceding call to calcImplicitValence() -85: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp -85: Failed Expression: d_implicitValence > -1 -85: **** -85: -85: [03:17:31] -85: -85: **** -85: Pre-condition Violation -85: getNumImplicitHs() called without preceding call to calcImplicitValence() -85: Violation occurred on line 291 in file ./Code/GraphMol/Atom.cpp -85: Failed Expression: d_implicitValence > -1 -85: **** +85: ........./build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> +85: png = open(fname, 'rb').read() +85: ResourceWarning: Enable tracemalloc to get the object allocation traceback +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 34 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 36 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 38 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 40 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 42 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 87 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 89 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 91 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 93 +85: [12:24:58] Found a SCD/SED line with missing/empty SDT specification at line 95 +86: ..[12:24:58] == testRGroupState +85: ..[12:24:58] SMARTS Parse Error: syntax error while parsing: boromicacid +85: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +85: [12:24:58] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +85: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +85: [12:24:58] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +85: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +85: [12:24:58] reaction has no reactants +85: [12:24:58] reaction has no products +85: [12:24:58] initialization failed +85: [12:24:58] reaction has no reactants +85: [12:24:58] reaction has no products +86: .[12:24:58] == testRandomEnumerateAllBBsLibrary +86: ** [1, 1] +86: ** [0, 2] +86: ** [1, 0] +85: .[12:24:58] SMARTS Parse Error: syntax error while parsing: boromicacid +85: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +85: [12:24:58] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +85: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +85: [12:24:58] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +85: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +85: [12:24:58] reaction has no reactants +85: [12:24:58] reaction has no products +85: [12:24:58] initialization failed +85: [12:24:58] reaction has no reactants +85: [12:24:58] reaction has no products +85: . +85: ---------------------------------------------------------------------- +85: Ran 50 tests in 0.364s 85: -86: .[03:17:31] == testEnumerateLibrary -86: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py:266: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/enumeration.pickle'> -86: open(os.path.join(self.dataDir, "enumeration.pickle"), 'rb').read()) -86: ResourceWarning: Enable tracemalloc to get the object allocation traceback -85: .......[03:17:31] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -85: [03:17:31] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -85: [03:17:31] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -85: [03:17:31] stereo atoms in input cannot be mapped to output (atoms are no longer bonded) -85: .[03:17:31] product atom-mapping number 1 found multiple times. -85: [03:17:31] product atom-mapping number 1 found multiple times. - 76/222 Test #87: pyChemReactionSanitize ................. Passed 0.42 sec +85: OK +85: ******************************************** +85: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn +85: +86: .[12:24:58] == testRandomEnumerateLibrary +86: .[12:24:58] == testRandomSample +86: .[12:24:58] == testRandomSampleAllBBs +86: .[12:24:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +86: [12:24:58] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +86: .[12:24:58] == testRemoveBadMatches +86: .[12:24:58] == testTimings + 76/222 Test #87: pyChemReactionSanitize ................. Passed 1.22 sec test 88 Start 88: testChemTransforms 88: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 88: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 88: Test timeout computed to be: 1500 -85: ................[03:17:31] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 3 -85: [03:17:31] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 3 88: 1 smi: CC 88: 1 smi: CC 88: 2 smi: CCO[C@H](N)P @@ -16638,82 +16738,25 @@ 88: replaceSub smi1:CCNCC 88: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 88: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -85: .[03:17:31] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 3 -85: ..[03:17:31] reactant 2 has no mapped atoms. -85: [03:17:31] reactant 2 has no mapped atoms. -85: [03:17:31] product 1 has no mapped atoms. -88: [03:17:31] SMARTS Parse Error: syntax error while parsing: bar -88: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' -86: ..[03:17:31] == testRGroupState -85: ........[03:17:31] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])Q -85: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])Q' for input: '[C:1](=[O:2])Q' -85: [03:17:31] SMARTS Parse Error: syntax error while parsing: [C:1](=[O:2])[N:3]Q -85: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=[O:2])[N:3]Q' for input: '[C:1](=[O:2])[N:3]Q' -85: .[03:17:31] reactant atom-mapping number 1 found multiple times. -85: [03:17:31] product atom-mapping number 2 not found in reactants. -85: [03:17:31] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 4 -85: [03:17:31] product atom-mapping number 5 not found in reactants. -86: .[03:17:31] == testRandomEnumerateAllBBsLibrary - 77/222 Test #88: testChemTransforms ..................... Passed 0.05 sec + 77/222 Test #85: pyChemReactions ........................ Passed 1.56 sec test 89 Start 89: chemTransformsTestCatch 89: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 89: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ChemTransforms 89: Test timeout computed to be: 1500 -86: ** [1, 1] -86: ** [0, 2] -86: ** [1, 0] -86: .[03:17:31] == testRandomEnumerateLibrary -85: ........./build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'> -85: png = open(fname, 'rb').read() -85: ResourceWarning: Enable tracemalloc to get the object allocation traceback -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 34 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 36 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 38 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 40 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 42 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 87 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 89 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 91 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 93 -85: [03:17:31] Found a SCD/SED line with missing/empty SDT specification at line 95 -86: .[03:17:31] == testRandomSample -85: ..[03:17:31] SMARTS Parse Error: syntax error while parsing: boromicacid -85: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -85: [03:17:31] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -85: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -85: [03:17:31] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -85: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -85: [03:17:31] reaction has no reactants -85: [03:17:31] reaction has no products -85: [03:17:31] initialization failed -85: [03:17:31] reaction has no reactants -85: [03:17:31] reaction has no products -85: .[03:17:31] SMARTS Parse Error: syntax error while parsing: boromicacid -85: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -85: [03:17:31] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -85: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -85: [03:17:31] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -85: [03:17:31] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -85: [03:17:31] reaction has no reactants -85: [03:17:31] reaction has no products -85: [03:17:31] initialization failed -85: [03:17:31] reaction has no reactants -85: [03:17:31] reaction has no products -85: . -85: ---------------------------------------------------------------------- -85: Ran 50 tests in 0.140s -85: -85: OK -85: ******************************************** -85: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testData/AmideBond.rxn -85: -89: Randomness seeded to: 1593581042 -89: [03:17:31] Incomplete atom labelling, cannot make bond -89: [03:17:31] +88: [12:24:58] SMARTS Parse Error: syntax error while parsing: bar +88: [12:24:58] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' + 78/222 Test #88: testChemTransforms ..................... Passed 0.14 sec +test 90 + Start 90: tautomerQueryTestCatch + +90: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch +90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery +90: Test timeout computed to be: 1500 +89: Randomness seeded to: 3761095658 +89: [12:24:58] Incomplete atom labelling, cannot make bond +89: [12:24:58] 89: 89: **** 89: Invariant Violation @@ -16722,9 +16765,8 @@ 89: Failed Expression: !bond.b 89: **** 89: -86: .[03:17:31] == testRandomSampleAllBBs -89: [03:17:31] Incomplete atom labelling, cannot make bond -89: [03:17:31] +89: [12:24:58] Incomplete atom labelling, cannot make bond +89: [12:24:58] 89: 89: **** 89: Invariant Violation @@ -16733,8 +16775,8 @@ 89: Failed Expression: !bond.b 89: **** 89: -89: [03:17:31] Incomplete atom labelling, cannot make bond -89: [03:17:31] +89: [12:24:58] Incomplete atom labelling, cannot make bond +89: [12:24:58] 89: 89: **** 89: Invariant Violation @@ -16743,21 +16785,10 @@ 89: Failed Expression: !bond.b 89: **** 89: - 78/222 Test #37: hanoiTest .............................. Passed 2.41 sec -test 90 - Start 90: tautomerQueryTestCatch - -90: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch -90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery -90: Test timeout computed to be: 1500 -86: .[03:17:31] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -86: [03:17:31] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -86: .[03:17:31] == testRemoveBadMatches -86: .[03:17:31] == testTimings -89: [03:17:31] Incomplete atom labelling, cannot make bond -89: [03:17:31] Incomplete atom labelling, cannot make bond -89: [03:17:31] Incomplete atom labelling, cannot make bond -89: [03:17:31] +89: [12:24:58] Incomplete atom labelling, cannot make bond +89: [12:24:58] Incomplete atom labelling, cannot make bond +89: [12:24:58] Incomplete atom labelling, cannot make bond +89: [12:24:58] 89: 89: **** 89: Invariant Violation @@ -16766,8 +16797,8 @@ 89: Failed Expression: !bond.b 89: **** 89: -89: [03:17:31] Incomplete atom labelling, cannot make bond -89: [03:17:31] +89: [12:24:58] Incomplete atom labelling, cannot make bond +89: [12:24:58] 89: 89: **** 89: Invariant Violation @@ -16776,7 +16807,7 @@ 89: Failed Expression: !bond.b 89: **** 89: -89: [03:17:31] +89: [12:24:59] 89: 89: **** 89: Invariant Violation @@ -16788,15 +16819,18 @@ 89: =============================================================================== 89: All tests passed (667 assertions in 7 test cases) 89: - 79/222 Test #89: chemTransformsTestCatch ................ Passed 0.09 sec + 79/222 Test #89: chemTransformsTestCatch ................ Passed 0.18 sec test 91 Start 91: pyTautomerQuery 91: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 91: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/TautomerQuery/Wrap 91: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... - 80/222 Test #85: pyChemReactions ........................ Passed 0.76 sec +90: Randomness seeded to: 2102958059 +90: =============================================================================== +90: All tests passed (93 assertions in 13 test cases) +90: + 80/222 Test #90: tautomerQueryTestCatch ................. Passed 0.38 sec test 92 Start 92: testSubgraphs1 @@ -16811,9 +16845,6 @@ 92: Finished 92: ----------------------- 92: testSubgraphs2 -25: All 191 tests passed -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 92: Finished 92: ----------------------- 92: Path retrieval @@ -16826,11 +16857,19 @@ 92: Finished 92: ----------------------- 92: testUniqueSubgraphs2 -90: Randomness seeded to: 1504194693 -90: =============================================================================== -90: All tests passed (93 assertions in 13 test cases) -90: - 81/222 Test #90: tautomerQueryTestCatch ................. Passed 0.17 sec +91: ..... +91: ---------------------------------------------------------------------- +91: Ran 5 tests in 0.092s +91: +91: OK +92: Finished +92: ----------------------- +92: testRootedSubgraphs +92: Finished +92: ----------------------- +92: testRootedPaths +92: Finished + 81/222 Test #92: testSubgraphs1 ......................... Passed 0.58 sec test 93 Start 93: testSubgraphs2 @@ -16852,30 +16891,57 @@ 93: ----------------------- 93: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 93: Finished - 82/222 Test #93: testSubgraphs2 ......................... Passed 0.03 sec + 82/222 Test #93: testSubgraphs2 ......................... Passed 0.07 sec test 94 Start 94: subgraphsCatch 94: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch 94: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Subgraphs 94: Test timeout computed to be: 1500 -11: .................. -11: ---------------------------------------------------------------------- -94: Randomness seeded to: 584863225 +94: Randomness seeded to: 2431028721 94: --------- 94: =============================================================================== 94: All tests passed (11 assertions in 1 test case) 94: - 83/222 Test #94: subgraphsCatch ......................... Passed 0.03 sec + 83/222 Test #94: subgraphsCatch ......................... Passed 0.07 sec test 95 Start 95: filterCatalogTest 95: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest 95: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog 95: Test timeout computed to be: 1500 -11: Ran 18 tests in 2.978s -11: -11: OK + 84/222 Test #91: pyTautomerQuery ........................ Passed 1.02 sec +test 96 + Start 96: pyFilterCatalog + +96: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +96: Test timeout computed to be: 1500 +86: . +86: ---------------------------------------------------------------------- +86: Ran 11 tests in 1.758s +86: +86: OK +86: True +86: == CartesianProductStrategy CartesianProductStrategy +86: 197 out of 300 +86: 0 6 out of 10 +86: 1 3 out of 5 +86: 2 4 out of 6 +86: 198 out of 300 +86: 0 10 out of 10 +86: 1 5 out of 5 +86: 2 6 out of 6 +86: Skipped 10000000 in 0.08736729621887207 seconds +86: Skipped 10000000 in 0.7259366512298584 seconds +86: Skipped 10000000 in 0.36695361137390137 seconds + 85/222 Test #37: hanoiTest .............................. Passed 6.57 sec +test 97 + Start 97: testFragCatalog + +97: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog +97: Test timeout computed to be: 1500 95: Warning: molecule failed filter 95: Warning: molecule failed filter: reason hzone_phenol_A(479) 95: v = { @@ -16964,147 +17030,137 @@ 95: 10,15}, 95: 11,16}, 95: } - 84/222 Test #11: pyBV ................................... Passed 3.28 sec -test 96 - Start 96: pyFilterCatalog - -96: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -96: Test timeout computed to be: 1500 -92: Finished -92: ----------------------- -92: testRootedSubgraphs -92: Finished -92: ----------------------- -92: testRootedPaths -92: Finished - 85/222 Test #92: testSubgraphs1 ......................... Passed 0.32 sec -test 97 - Start 97: testFragCatalog - -97: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog -97: Test timeout computed to be: 1500 -91: ..... -91: ---------------------------------------------------------------------- -91: Ran 5 tests in 0.031s -91: -91: OK 97: 21 -86: . -86: ---------------------------------------------------------------------- -86: Ran 11 tests in 0.636s -86: -86: OK -86: True -86: == CartesianProductStrategy CartesianProductStrategy -86: 197 out of 300 -86: 0 6 out of 10 -86: 1 3 out of 5 -86: 2 4 out of 6 -86: 198 out of 300 -86: 0 10 out of 10 -86: 1 5 out of 5 -86: 2 6 out of 6 -86: Skipped 10000000 in 0.0354461669921875 seconds -86: Skipped 10000000 in 0.25104808807373047 seconds -86: Skipped 10000000 in 0.07329177856445312 seconds - 86/222 Test #91: pyTautomerQuery ........................ Passed 0.49 sec + 86/222 Test #86: pyChemReactionEnumerations ............. Passed 2.90 sec test 98 Start 98: pyFragCatalog 98: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FragCatalog/Wrap 98: Test timeout computed to be: 1500 - 87/222 Test #86: pyChemReactionEnumerations ............. Passed 1.15 sec + 87/222 Test #95: filterCatalogTest ...................... Passed 0.56 sec test 99 Start 99: testDescriptors 99: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testDescriptors 99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 99: Test timeout computed to be: 1500 - 88/222 Test #95: filterCatalogTest ...................... Passed 0.31 sec +99: [12:25:00] ------------------------------------- +99: [12:25:00] Test Crippen parameter acquisition. +99: [12:25:00] done +99: [12:25:00] ------------------------------------- +99: [12:25:00] Test Crippen calculation. +99: [12:25:00] done +99: [12:25:00] ------------------------------------- +99: [12:25:00] Test Issue262: problems with Crippen calculation from pickles. +99: [12:25:00] done +99: [12:25:00] ------------------------------------- +99: [12:25:00] Test AMW calculation. +99: [12:25:00] done +99: [12:25:00] ------------------------------------- +99: [12:25:00] Test Exact MW calculation. +99: [12:25:00] done +99: [12:25:00] ------------------------------------- +99: [12:25:00] Test Labute ASA descriptors. +99: [12:25:00] done +99: [12:25:00] ------------------------------------- +99: [12:25:00] Test TPSA descriptors. +99: [12:25:00] done +99: [12:25:00] ------------------------------------- +99: [12:25:00] Test Lipinski parameters. +11: .................. +11: ---------------------------------------------------------------------- +11: Ran 18 tests in 7.762s +11: +11: OK + 88/222 Test #11: pyBV ................................... Passed 8.52 sec test 100 Start 100: testAUTOCORR2D 100: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D 100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 100: Test timeout computed to be: 1500 -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test Crippen parameter acquisition. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test Crippen calculation. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test Issue262: problems with Crippen calculation from pickles. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test AMW calculation. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test Exact MW calculation. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test Labute ASA descriptors. -100: [03:17:32] ---------------------------- +100: [12:25:00] ---------------------------- 100: start test autocorr2D -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test TPSA descriptors. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test Lipinski parameters. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test VSA descriptors. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test molecular formula calculation. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test Issue 3415534. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test Issue3433771: Bad definition for Crippen atom type O11. -99: [03:17:32] done -99: [03:17:32] ------------------------------------- -99: [03:17:32] Test multithreading +99: [12:25:01] done +99: [12:25:01] ------------------------------------- +99: [12:25:01] Test VSA descriptors. +99: [12:25:01] done +99: [12:25:01] ------------------------------------- +99: [12:25:01] Test molecular formula calculation. +99: [12:25:01] done +99: [12:25:01] ------------------------------------- +99: [12:25:01] Test Issue 3415534. +99: [12:25:01] done +99: [12:25:01] ------------------------------------- +99: [12:25:01] Test Issue3433771: Bad definition for Crippen atom type O11. +99: [12:25:01] done +99: [12:25:01] ------------------------------------- +99: [12:25:01] Test multithreading 99: reading molecules -99: processing -99: launch :0 -99: launch :1 -99: launch :2 -99: launch :3 -100: [03:17:32] done -100: [03:17:32] ------------------------------------- -100: [03:17:32] Test Github #3806: NaNs from AUTOCORR2D descriptor -100: [03:17:32] done - 89/222 Test #100: testAUTOCORR2D ......................... Passed 0.29 sec + 89/222 Test #39: resMolSupplierTest ..................... Passed 7.43 sec test 101 Start 101: testATF 101: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testATF 101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 - 90/222 Test #101: testATF ................................ Passed 0.04 sec +99: processing +99: launch :0 +99: launch :1 +99: launch :2 +99: launch :3 + 90/222 Test #101: testATF ................................ Passed 0.07 sec test 102 Start 102: testBCUT 102: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testBCUT 102: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 -102: [03:17:32] ------------------------------------- -102: [03:17:32] Basic BCUT tests. -102: [03:17:32] done -102: [03:17:32] ------------------------------------- -102: [03:17:32] Larger BCUT tests. +102: [12:25:01] ------------------------------------- +102: [12:25:01] Basic BCUT tests. +102: [12:25:01] done +102: [12:25:01] ------------------------------------- +102: [12:25:01] Larger BCUT tests. +100: [12:25:01] done +100: [12:25:01] ------------------------------------- +100: [12:25:01] Test Github #3806: NaNs from AUTOCORR2D descriptor +100: [12:25:01] done + 91/222 Test #100: testAUTOCORR2D ......................... Passed 0.30 sec +test 103 + Start 103: testEEM + +103: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM +103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors +103: Test timeout computed to be: 1500 98: ......... 98: ---------------------------------------------------------------------- -98: Ran 9 tests in 0.067s +98: Ran 9 tests in 0.162s 98: 98: OK -97: [03:17:32] +103: =>start test EEM +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: 0 +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +97: [12:25:01] 97: 97: **** 97: Invariant Violation @@ -17113,7 +17169,7 @@ 97: Failed Expression: token != tokens.end() 97: **** 97: -97: [03:17:32] +97: [12:25:01] 97: 97: **** 97: Invariant Violation @@ -17122,7 +17178,7 @@ 97: Failed Expression: token != tokens.end() 97: **** 97: -97: [03:17:32] +97: [12:25:01] 97: 97: **** 97: Invariant Violation @@ -17131,708 +17187,665 @@ 97: Failed Expression: token != tokens.end() 97: **** 97: - 91/222 Test #97: testFragCatalog ........................ Passed 0.66 sec -test 103 - Start 103: testEEM - -103: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testEEM -103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors -103: Test timeout computed to be: 1500 - 92/222 Test #39: resMolSupplierTest ..................... Passed 3.41 sec + 92/222 Test #97: testFragCatalog ........................ Passed 1.27 sec test 104 Start 104: testPBF 104: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testPBF 104: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 104: Test timeout computed to be: 1500 -103: =>start test EEM -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: 0 -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [03:17:32] ------------------------------------- -104: [03:17:32] Basic PBF tests. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 93/222 Test #98: pyFragCatalog .......................... Passed 0.58 sec +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [12:25:01] ------------------------------------- +104: [12:25:01] Basic PBF tests. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 93/222 Test #98: pyFragCatalog .......................... Passed 1.13 sec test 105 Start 105: testRDFcustom 105: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 105: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 105: Test timeout computed to be: 1500 -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: 100 -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: 200 -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [03:17:32] done -104: [03:17:32] ------------------------------------- -104: [03:17:32] PBF edge cases. -104: [03:17:32] done - 94/222 Test #104: testPBF ................................ Passed 0.22 sec +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [12:25:01] done +104: [12:25:01] ------------------------------------- +104: [12:25:01] PBF edge cases. +104: [12:25:01] done + 94/222 Test #104: testPBF ................................ Passed 0.26 sec test 106 Start 106: testRDF 106: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testRDF 106: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 106: Test timeout computed to be: 1500 -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: [03:17:32] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -63: [03:17:32] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: 100 +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: 200 +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 300 -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -105: =>start test rdf custom -105: [03:17:33] test on : 365 molecules done -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: 400 -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: ---------------------------------- -63: ---------------------------------- -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: [03:17:33] -63: -63: **** -63: Pre-condition Violation -63: rlabel out of range for MDL files -63: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp -63: Failed Expression: rlabel >= 0 && rlabel < 100 -63: **** -63: -63: [03:17:33] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: Elapsed time: 0.37879 s -103: Errors:0 -103: [03:17:33] test on : 500 molecules done - 95/222 Test #103: testEEM ................................ Passed 0.41 sec +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +106: =>start test rdf +106: [12:25:02] test on : 365 molecules done +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 95/222 Test #106: testRDF ................................ Passed 0.88 sec test 107 Start 107: testMORSE 107: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testMORSE 107: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 107: Test timeout computed to be: 1500 -102: [03:17:33] ------------------------------------- -102: [03:17:33] Test empty molecule BCUT. - 96/222 Test #102: testBCUT ............................... Passed 0.59 sec +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105: =>start test rdf custom +105: [12:25:02] test on : 365 molecules done +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +102: [12:25:02] ------------------------------------- +102: [12:25:02] Test empty molecule BCUT. + 96/222 Test #102: testBCUT ............................... Passed 1.48 sec test 108 Start 108: test3D 108: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/test3D 108: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 108: Test timeout computed to be: 1500 -108: [03:17:33] ------------------------------------- -108: [03:17:33] Basic PMI tests. -96: .............[03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -96: [03:17:33] SMILES Parse Error: syntax error while parsing: --- -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' -96: [03:17:33] dasfsadf -63: [03:17:33] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -63: [03:17:33] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -63: [03:17:33] Empty atom list: 'M ALS 1 0 F' on line 8. -63: de_DE.UTF-8 -63: [03:17:33] ------------------------------------- -63: [03:17:33] Test multithreading Locale Switching -105: =>start test morse custom -105: [03:17:33] test on : 365 molecules done -96: .[03:17:33] SMILES Parse Error: syntax error while parsing: mydoghasfleas -96: [03:17:33] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' -108: [03:17:33] done -108: [03:17:33] ------------------------------------- -108: [03:17:33] More PMI/NPR tests. -108: [03:17:33] done -108: [03:17:33] ------------------------------------- -108: [03:17:33] Basic NPR tests. -106: =>start test rdf -106: [03:17:33] test on : 365 molecules done - 97/222 Test #106: testRDF ................................ Passed 0.44 sec +66: [12:25:02] Finished: testSmiCorrectness() +66: [12:25:02] ----------------------------------------- +66: +66: [12:25:02] +66: ----------------------------------------- +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: 400 +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +108: [12:25:02] ------------------------------------- +108: [12:25:02] Basic PMI tests. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +66: [12:25:02] Spurious data before the first property will be ignored +66: [12:25:02] Property will be truncated after the first blank line +66: [12:25:02] Property will be truncated after the first blank line +66: [12:25:02] Property will be truncated after the first blank line +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +25: All 191 tests passed +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [12:25:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: Elapsed time: 1.54565 s +103: Errors:0 +103: [12:25:02] test on : 500 molecules done + 97/222 Test #103: testEEM ................................ Passed 1.61 sec test 109 Start 109: testWHIM 109: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testWHIM 109: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 109: Test timeout computed to be: 1500 -63: [03:17:33] Test multithreading (Done) -63: [03:17:33] ------------------------------------- -63: *************************************** -63: *************************************** -63: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: [03:17:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: [03:17:33] bond with order 0 found on line 7. This is not part of the MDL specification. +96: .............[12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +96: [12:25:02] SMILES Parse Error: syntax error while parsing: --- +96: [12:25:02] SMILES Parse Error: Failed parsing SMILES '---' for input: '---' +96: [12:25:02] dasfsadf +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... +108: [12:25:03] done +108: [12:25:03] ------------------------------------- +108: [12:25:03] More PMI/NPR tests. +108: [12:25:03] done +108: [12:25:03] ------------------------------------- +108: [12:25:03] Basic NPR tests. +96: .[12:25:03] SMILES Parse Error: syntax error while parsing: mydoghasfleas +96: [12:25:03] SMILES Parse Error: Failed parsing SMILES 'mydoghasfleas' for input: 'mydoghasfleas' +63: [12:25:03] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +63: [12:25:03] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 96: ....... 96: ---------------------------------------------------------------------- -96: Ran 21 tests in 1.005s +96: Ran 21 tests in 2.434s 96: 96: OK 96: (Five aromatic carbons And (Not any of Five aromatic carbons)) @@ -17854,97 +17867,105 @@ 96: 1 96: 2 96: running -108: [03:17:33] done -108: [03:17:33] ------------------------------------- -108: [03:17:33] PMI edge cases. -108: [03:17:33] done -108: [03:17:33] ------------------------------------- -108: [03:17:33] NPR edge cases. -108: [03:17:33] done -108: [03:17:33] ------------------------------------- -108: [03:17:33] 3D descriptors. -108: [03:17:33] done -108: [03:17:33] ------------------------------------- -108: [03:17:33] 3D descriptor edge cases. -108: [03:17:33] done -108: [03:17:33] ------------------------------------- -108: [03:17:33] Inertial shape factor. -108: [03:17:33] done - 98/222 Test #108: test3D ................................. Passed 0.35 sec +63: ---------------------------------- +63: ---------------------------------- +63: [12:25:03] +63: +63: **** +63: Pre-condition Violation +63: rlabel out of range for MDL files +63: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp +63: Failed Expression: rlabel >= 0 && rlabel < 100 +63: **** +63: +63: [12:25:03] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +108: [12:25:03] done +108: [12:25:03] ------------------------------------- +108: [12:25:03] PMI edge cases. +108: [12:25:03] done +108: [12:25:03] ------------------------------------- +108: [12:25:03] NPR edge cases. +108: [12:25:03] done +108: [12:25:03] ------------------------------------- +108: [12:25:03] 3D descriptors. +108: [12:25:03] done +108: [12:25:03] ------------------------------------- +108: [12:25:03] 3D descriptor edge cases. +108: [12:25:03] done +108: [12:25:03] ------------------------------------- +108: [12:25:03] Inertial shape factor. +108: [12:25:03] done + 98/222 Test #108: test3D ................................. Passed 0.85 sec test 110 Start 110: testGETAWAY 110: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 110: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 110: Test timeout computed to be: 1500 -63: [03:17:33] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -63: [03:17:33] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -63: [03:17:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -63: generating smiles -63: 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 -63: converting back -63: check isomorphism - 99/222 Test #96: pyFilterCatalog ........................ Passed 1.61 sec +66: [12:25:03] Finished: testSDCorrectness() +66: [12:25:03] ----------------------------------------- +66: + 99/222 Test #66: testMultithreadedMolSupplier ........... Passed 8.22 sec test 111 Start 111: testAUTOCORR3D 111: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 111: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 -109: =>start test WHIM -109: [03:17:33] test on : 365 molecules done -100/222 Test #109: testWHIM ............................... Passed 0.26 sec +100/222 Test #96: pyFilterCatalog ........................ Passed 3.68 sec test 112 Start 112: testCoulombMat 112: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 112: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -112: ===================== Testing CoulombMat ======================= -105: =>start test AUTOCORR3D custom -105: [03:17:33] test on : 365 molecules done -112: CM test 1 mat Done -101/222 Test #112: testCoulombMat ......................... Passed 0.02 sec +109: =>start test WHIM +109: [12:25:03] test on : 365 molecules done +101/222 Test #109: testWHIM ............................... Passed 0.85 sec test 113 Start 113: descriptorsTestCatch 113: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 113: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 -113: Randomness seeded to: 3344237575 -113: =============================================================================== -113: All tests passed (482 assertions in 7 test cases) -113: -102/222 Test #113: descriptorsTestCatch ................... Passed 0.03 sec +112: ===================== Testing CoulombMat ======================= +112: CM test 1 mat Done +102/222 Test #112: testCoulombMat ......................... Passed 0.09 sec test 114 Start 114: pyMolDescriptors 114: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 114: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 114: Test timeout computed to be: 1500 -105: =>start test 2 WHIM custom -105: [03:17:33] test on : 365 molecules done -105: =>start test 1 WHIM custom -105: [03:17:33] test on : 365 molecules done -107: =>start test MORSE -107: =>read file -107: [03:17:33] test on : 365 molecules done -103/222 Test #107: testMORSE .............................. Passed 0.80 sec +113: Randomness seeded to: 2321987437 +113: =============================================================================== +113: All tests passed (482 assertions in 7 test cases) +113: +103/222 Test #113: descriptorsTestCatch ................... Passed 0.12 sec test 115 Start 115: pyMolDescriptors3D 115: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/test3D.py" 115: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Descriptors/Wrap 115: Test timeout computed to be: 1500 -111: =>start test autocorr3D -111: [03:17:34] test on : 365 molecules done -104/222 Test #111: testAUTOCORR3D ......................... Passed 0.40 sec +105: =>start test morse custom +105: [12:25:03] test on : 365 molecules done +63: [12:25:04] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +63: [12:25:04] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +107: =>start test MORSE +107: =>read file +107: [12:25:04] test on : 365 molecules done +104/222 Test #107: testMORSE .............................. Passed 1.63 sec test 116 Start 116: testFingerprints 116: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 116: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 116: Test timeout computed to be: 1500 +63: [12:25:04] Empty atom list: 'M ALS 1 0 F' on line 8. +63: de_DE.UTF-8 +63: [12:25:04] ------------------------------------- +63: [12:25:04] Test multithreading Locale Switching 116: 116: 116: @@ -18379,6 +18400,10 @@ 116: 4 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 5 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 6 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 3 arom?: 1 chi: 0 +63: [12:25:04] Test multithreading (Done) +63: [12:25:04] ------------------------------------- +63: *************************************** +63: *************************************** 116: 7 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 8 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 116: 9 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 @@ -18428,107 +18453,188 @@ 116: 116: ------------------- 116: -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Morgan Fingerprints. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Morgan Fingerprints using fromAtoms argument. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Morgan Fingerprints as bit vects. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Morgan Fingerprints with feature invariants. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test additional Morgan fingerprints options. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Atom Codes. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Atom Pairs. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Atom Pairs part 2. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Topological Torsions. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Bulk Topological Torsions. -63: [03:17:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [03:17:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [03:17:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [03:17:34] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [03:17:34] deprecated group abbreviation ignored on line 24 -63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -63: [03:17:34] -63: -63: **** -63: Post-condition Violation -63: Element 'Mv' not found -63: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -63: Failed Expression: anum > -1 -63: **** -63: -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Hashed Atom Pairs. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Hashed torsions. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Rooted Atom Pairs. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test ignoring atoms in Atom Pairs. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Rooted Topological Torsions. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test ignoring atoms in Topological Torsions. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test atom info from morgan fingerprints. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test atom info from morgan fingerprints including Info Redundant Environments. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] ------------------------------------- -116: [03:17:34] ------------------------------------- -116: [03:17:34] ------------------------------------- -116: [03:17:34] ------------------------------------- -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Atom Pairs including info about chirality. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test Topological Torsions including info about chirality. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test GitHub Issue 25: fingerprint backwards compatibility. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test GitHub Issue 151: PatternFingerprint problems -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test 3D atom pairs. -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -116: [03:17:34] done -116: [03:17:34] ------------------------------------- -116: [03:17:34] Test multithreading with the pattern FP +63: [12:25:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +63: [12:25:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Morgan Fingerprints. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Morgan Fingerprints using fromAtoms argument. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Morgan Fingerprints as bit vects. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Morgan Fingerprints with feature invariants. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test additional Morgan fingerprints options. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Atom Codes. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Atom Pairs. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Atom Pairs part 2. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Topological Torsions. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Bulk Topological Torsions. +63: [12:25:04] bond with order 0 found on line 7. This is not part of the MDL specification. +63: [12:25:04] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +63: [12:25:04] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +63: [12:25:04] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +63: generating smiles +63: 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 +63: converting back +63: check isomorphism +111: =>start test autocorr3D +111: [12:25:04] test on : 365 molecules done +105/222 Test #111: testAUTOCORR3D ......................... Passed 0.74 sec +test 117 + Start 117: testMHFPFingerprint + +117: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint +117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints +117: Test timeout computed to be: 1500 +117: [12:25:04] ------------------------------------- +117: [12:25:04] Test MHFP fingerprint encoder initialization +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Hashed Atom Pairs. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Hashed torsions. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Rooted Atom Pairs. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test ignoring atoms in Atom Pairs. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Rooted Topological Torsions. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test ignoring atoms in Topological Torsions. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test atom info from morgan fingerprints. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test atom info from morgan fingerprints including Info Redundant Environments. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] ------------------------------------- +116: [12:25:04] ------------------------------------- +117: [12:25:04] done +117: [12:25:04] ------------------------------------- +117: [12:25:04] Test MHFP shingling creation +116: [12:25:04] ------------------------------------- +116: [12:25:04] ------------------------------------- +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Atom Pairs including info about chirality. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test Topological Torsions including info about chirality. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test GitHub Issue 25: fingerprint backwards compatibility. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test GitHub Issue 151: PatternFingerprint problems +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test 3D atom pairs. +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +116: [12:25:04] done +116: [12:25:04] ------------------------------------- +116: [12:25:04] Test multithreading with the pattern FP 116: reading molecules +105: =>start test AUTOCORR3D custom +105: [12:25:04] test on : 365 molecules done +117: [12:25:04] done +117: [12:25:04] ------------------------------------- +117: [12:25:04] Test MHFP hashing of string and uint arrays +117: [12:25:04] done +117: [12:25:04] ------------------------------------- +117: [12:25:04] Test SECFP fingerprint functionality +117: [12:25:04] done +106/222 Test #117: testMHFPFingerprint .................... Passed 0.17 sec +test 118 + Start 118: testFingerprintGenerators + +118: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators +118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints +118: Test timeout computed to be: 1500 116: pass 1 116: launch :0 116: launch :1 116: launch :2 116: launch :3 -114: .....[03:17:34] +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test atom-pair fp generator +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test atom-pair fp generator with different arguments +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test atom-pair additional output +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test Folded Atom Pairs. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test Rooted Atom Pairs. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test ignoring atoms in Atom Pairs. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test Atom Pairs including info about chirality. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test Morgan Fingerprints. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test morgan fp generator +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test Morgan Fingerprints using fromAtoms argument. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test Morgan Fingerprints as bit vects. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test Morgan Fingerprints with feature invariants. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test additional Morgan fingerprints options. +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Single atoms setting radius 1 bits in Morgan fingerprints +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test different invariant generator combinations +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test invariant overriding +118: [12:25:04] done +118: [12:25:04] ------------------------------------- +118: [12:25:04] Test RDKit fp generator +114: .....[12:25:04] 114: 114: **** 114: Pre-condition Violation @@ -18539,7 +18645,7 @@ 114: 114: ......................... 114: ---------------------------------------------------------------------- -114: Ran 30 tests in 0.043s +114: Ran 30 tests in 0.114s 114: 114: OK 114: exactmw 78.046950192 @@ -18587,297 +18693,187 @@ 114: Phi 0.9130327103921437 114: exactmw 78.046950192 114: lipinskiHBA 0.0 -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test Issue252: Bad definitions for Crippen atom types. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test calculation of ChiVs. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test calculation of ChiNs. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test calculation of HallKierAlpha. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test calculation of Kappa1. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test calculation of Kappa2. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test calculation of Kappa3. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test Crippen atom type calculations. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test ring descriptors -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test other count descriptors. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test MQN -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test GitHub Issue 56. -99: [03:17:34] WARNING: not removing hydrogen atom without neighbors -99: [03:17:34] WARNING: not removing hydrogen atom without neighbors -99: [03:17:34] WARNING: not removing hydrogen atom without neighbors -99: [03:17:34] WARNING: not removing hydrogen atom without neighbors -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test Github92: Bad Crippen atom type for pyrrole H. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test Github362: order dependence in Kier-Hall descriptors. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test calculation of spiro and bridgehead counts. -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test Github694: ExactMolWt ignoring the mass of the electron -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Testing Properties and KitchenSink -99: [03:17:34] ---Caught keyerror (bad property name)--- -99: [03:17:34] ---Caught stereo value error--- -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test USR Descriptor -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test Github #1973: support P and S terms for TPSA calculation -99: [03:17:34] done -99: [03:17:34] ------------------------------------- -99: [03:17:34] Test Github #2948: Empty molecule has non-zero LabuteASA -99: [03:17:34] done -105/222 Test #99: testDescriptors ........................ Passed 2.10 sec -test 117 - Start 117: testMHFPFingerprint - -117: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint -117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints -117: Test timeout computed to be: 1500 -117: [03:17:34] ------------------------------------- -117: [03:17:34] Test MHFP fingerprint encoder initialization -117: [03:17:34] done -117: [03:17:34] ------------------------------------- -117: [03:17:34] Test MHFP shingling creation -106/222 Test #114: pyMolDescriptors ....................... Passed 0.64 sec -test 118 - Start 118: testFingerprintGenerators - -118: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators -118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints -118: Test timeout computed to be: 1500 +115: ........ +115: ---------------------------------------------------------------------- +115: Ran 8 tests in 0.367s +115: +115: OK 116: pass 2 116: launch :0 116: launch :1 116: launch :2 116: launch :3 -117: [03:17:34] done -117: [03:17:34] ------------------------------------- -117: [03:17:34] Test MHFP hashing of string and uint arrays -117: [03:17:34] done -117: [03:17:34] ------------------------------------- -117: [03:17:34] Test SECFP fingerprint functionality -117: [03:17:34] done -107/222 Test #117: testMHFPFingerprint .................... Passed 0.04 sec +105: =>start test 2 WHIM custom +105: [12:25:05] test on : 365 molecules done +107/222 Test #114: pyMolDescriptors ....................... Passed 1.45 sec test 119 Start 119: fpTestCatch 119: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 119: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 119: Test timeout computed to be: 1500 -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test atom-pair fp generator -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test atom-pair fp generator with different arguments -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -119: Randomness seeded to: 2878829171 -119: =============================================================================== -119: All tests passed (166 assertions in 14 test cases) -119: -108/222 Test #119: fpTestCatch ............................ Passed 0.04 sec +108/222 Test #115: pyMolDescriptors3D ..................... Passed 1.44 sec test 120 Start 120: fpGenTestCatch 120: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch 120: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints 120: Test timeout computed to be: 1500 -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test atom-pair additional output -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Folded Atom Pairs. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Rooted Atom Pairs. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test ignoring atoms in Atom Pairs. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Atom Pairs including info about chirality. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Morgan Fingerprints. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test morgan fp generator -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Morgan Fingerprints using fromAtoms argument. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Morgan Fingerprints as bit vects. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Morgan Fingerprints with feature invariants. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test additional Morgan fingerprints options. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Single atoms setting radius 1 bits in Morgan fingerprints -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test different invariant generator combinations -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test invariant overriding -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test RDKit fp generator -115: ........ -115: ---------------------------------------------------------------------- -115: Ran 8 tests in 0.123s -115: -115: OK -109/222 Test #115: pyMolDescriptors3D ..................... Passed 0.60 sec +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test Issue252: Bad definitions for Crippen atom types. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test calculation of ChiVs. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test calculation of ChiNs. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test calculation of HallKierAlpha. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test calculation of Kappa1. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test calculation of Kappa2. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test calculation of Kappa3. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test Crippen atom type calculations. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test ring descriptors +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test other count descriptors. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test MQN +119: Randomness seeded to: 3715877117 +119: =============================================================================== +119: All tests passed (166 assertions in 14 test cases) +119: +109/222 Test #119: fpTestCatch ............................ Passed 0.09 sec test 121 Start 121: pyTestGenerator 121: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 121: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 121: Test timeout computed to be: 1500 -120: Randomness seeded to: 336160017 -120: =============================================================================== -120: All tests passed (2678 assertions in 4 test cases) -120: -110/222 Test #120: fpGenTestCatch ......................... Passed 0.16 sec +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test GitHub Issue 56. +99: [12:25:05] WARNING: not removing hydrogen atom without neighbors +99: [12:25:05] WARNING: not removing hydrogen atom without neighbors +99: [12:25:05] WARNING: not removing hydrogen atom without neighbors +99: [12:25:05] WARNING: not removing hydrogen atom without neighbors +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test Github92: Bad Crippen atom type for pyrrole H. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test Github362: order dependence in Kier-Hall descriptors. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test calculation of spiro and bridgehead counts. +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test Github694: ExactMolWt ignoring the mass of the electron +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Testing Properties and KitchenSink +99: [12:25:05] ---Caught keyerror (bad property name)--- +99: [12:25:05] ---Caught stereo value error--- +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test USR Descriptor +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test Github #1973: support P and S terms for TPSA calculation +99: [12:25:05] done +99: [12:25:05] ------------------------------------- +99: [12:25:05] Test Github #2948: Empty molecule has non-zero LabuteASA +99: [12:25:05] done +110/222 Test #99: testDescriptors ........................ Passed 4.80 sec test 122 Start 122: pyTestMHFP 122: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 122: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Fingerprints/Wrap 122: Test timeout computed to be: 1500 -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test unfolded version of RDKFP -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test topological torsion fp generator -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Topological Torsions. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Folded torsions. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Bulk Topological Torsions. -66: [03:17:34] Finished: testSmiCorrectness() -66: [03:17:34] ----------------------------------------- -66: -66: [03:17:34] -66: ----------------------------------------- -66: [03:17:34] Spurious data before the first property will be ignored -66: [03:17:34] Property will be truncated after the first blank line -66: [03:17:34] Property will be truncated after the first blank line -66: [03:17:34] Property will be truncated after the first blank line -121: ............. -121: ---------------------------------------------------------------------- -121: Ran 13 tests in 0.125s -121: -121: OK -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Rooted Topological Torsions. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test ignoring atoms in Topological Torsions. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test Topological Torsions including info about chirality. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test GitHub Issue 25: fingerprint backwards compatibility. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -118: [03:17:34] done -118: [03:17:34] ------------------------------------- -118: [03:17:34] Test convenience and bulk fp calculation functions -122: .. -122: ---------------------------------------------------------------------- -122: Ran 2 tests in 0.038s -122: -122: OK -111/222 Test #121: pyTestGenerator ........................ Passed 0.53 sec +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test unfolded version of RDKFP +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test topological torsion fp generator +120: Randomness seeded to: 1457324359 +120: =============================================================================== +120: All tests passed (2678 assertions in 4 test cases) +120: +111/222 Test #120: fpGenTestCatch ......................... Passed 0.27 sec test 123 Start 123: testPartialCharges 123: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 123: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges 123: Test timeout computed to be: 1500 -105: =>start test GETAWAY custom -105: [03:17:35] test on : 365 molecules done -112/222 Test #105: testRDFcustom .......................... Passed 2.30 sec +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test Topological Torsions. +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test Folded torsions. +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test Bulk Topological Torsions. +112/222 Test #123: testPartialCharges ..................... Passed 0.07 sec test 124 Start 124: pyPartialCharges 124: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 124: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/PartialCharges/Wrap 124: Test timeout computed to be: 1500 -110: =>start test GETAWAY -110: [03:17:35] test on : 365 molecules done -113/222 Test #110: testGETAWAY ............................ Passed 1.59 sec -114/222 Test #123: testPartialCharges ..................... Passed 0.04 sec +105: =>start test 1 WHIM custom +105: [12:25:05] test on : 365 molecules done +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test Rooted Topological Torsions. +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test ignoring atoms in Topological Torsions. +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test Topological Torsions including info about chirality. +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test GitHub Issue 25: fingerprint backwards compatibility. +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +118: [12:25:05] done +118: [12:25:05] ------------------------------------- +118: [12:25:05] Test convenience and bulk fp calculation functions +122: .. +122: ---------------------------------------------------------------------- +122: Ran 2 tests in 0.039s +122: +122: OK +113/222 Test #122: pyTestMHFP ............................. Passed 0.70 sec test 125 Start 125: testMolTransforms 125: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 125: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms 125: Test timeout computed to be: 1500 -test 126 - Start 126: pyMolTransforms - -126: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" -126: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap -126: Test timeout computed to be: 1500 -115/222 Test #122: pyTestMHFP ............................. Passed 0.56 sec -test 127 - Start 127: testMMFFForceFieldHelpers - -127: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers -127: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF -127: Test timeout computed to be: 1500 125: *********************************************************** 125: Testing MolTransforms 125: --------------------------------- @@ -18908,25 +18904,92 @@ 125: testWeightedCentroid 125: 125: *********************************************************** -116/222 Test #125: testMolTransforms ...................... Passed 0.06 sec +114/222 Test #125: testMolTransforms ...................... Passed 0.13 sec +test 126 + Start 126: pyMolTransforms + +126: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" +126: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolTransforms/Wrap +126: Test timeout computed to be: 1500 +63: [12:25:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [12:25:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [12:25:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [12:25:06] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [12:25:06] deprecated group abbreviation ignored on line 24 +63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +63: [12:25:06] +63: +63: **** +63: Post-condition Violation +63: Element 'Mv' not found +63: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +63: Failed Expression: anum > -1 +63: **** +63: +121: ............. +121: ---------------------------------------------------------------------- +121: Ran 13 tests in 0.250s +121: +121: OK +124: ....... +124: ---------------------------------------------------------------------- +124: Ran 7 tests in 0.147s +124: +124: OK +115/222 Test #124: pyPartialCharges ....................... Passed 0.93 sec +test 127 + Start 127: testMMFFForceFieldHelpers + +127: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers +127: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF +127: Test timeout computed to be: 1500 +118: [12:25:06] done +118: [12:25:06] ------------------------------------- +118: [12:25:06] Test GitHub Issue #6958 +127: [12:25:06] ------------------------------------- +127: [12:25:06] Test MMFF atom types. +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing MMFF builder tools. +116/222 Test #118: testFingerprintGenerators .............. Passed 1.98 sec test 128 Start 128: testMMFFForceFieldHelpersMultiThread 128: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 128: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 128: Test timeout computed to be: 1500 -25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -127: [03:17:35] ------------------------------------- -127: [03:17:35] Test MMFF atom types. -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing MMFF builder tools. -128: [03:17:35] ------------------------------------- -128: [03:17:35] Test MMFF multithreading -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing MMFF builder+minimization. -25: All 191 tests passed +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing MMFF builder+minimization. +117/222 Test #121: pyTestGenerator ........................ Passed 1.27 sec +test 129 + Start 129: testUFFForceFieldHelpers + +129: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +129: Test timeout computed to be: 1500 +128: [12:25:06] ------------------------------------- +128: [12:25:06] Test MMFF multithreading +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing Issue239. +129: [12:25:06] ------------------------------------- +129: [12:25:06] Test UFF atom labels. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Test UFF atom typer. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing UFF builder tools. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing UFF builder+minimization. +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing calcEnergy with passed coords. +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing calcGrad. 128: processing 128: launch :0 128: launch :1 @@ -18952,570 +19015,586 @@ 128: launch :21 128: launch :22 128: launch :23 -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing Issue239. -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing calcEnergy with passed coords. -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing calcGrad. -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing Issue242. -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing github 308: crash during MMFF parameterization . -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing SFIssue1653802. -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Testing SFIssue2378119. -127: [03:17:35] done -127: [03:17:35] ------------------------------------- -127: [03:17:35] Test MMFF force-field parameter getters. -127: [03:17:35] ------------------------------------- -127: [03:17:35] Test MMFF multithreading +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing Issue242. +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing github 308: crash during MMFF parameterization . +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing SFIssue1653802. +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Testing SFIssue2378119. +127: [12:25:06] done +127: [12:25:06] ------------------------------------- +127: [12:25:06] Test MMFF force-field parameter getters. +127: [12:25:06] ------------------------------------- +127: [12:25:06] Test MMFF multithreading 127: generating reference data -118: [03:17:35] done -118: [03:17:35] ------------------------------------- -118: [03:17:35] Test GitHub Issue #6958 -117/222 Test #118: testFingerprintGenerators .............. Passed 0.98 sec -test 129 - Start 129: testUFFForceFieldHelpers - -129: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -129: Test timeout computed to be: 1500 -124: ....... -124: ---------------------------------------------------------------------- -124: Ran 7 tests in 0.054s -124: -124: OK -129: [03:17:35] ------------------------------------- -129: [03:17:35] Test UFF atom labels. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Test UFF atom typer. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing UFF builder tools. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing UFF builder+minimization. -66: [03:17:35] Finished: testSDCorrectness() -66: [03:17:35] ----------------------------------------- -66: -118/222 Test #66: testMultithreadedMolSupplier ........... Passed 5.38 sec +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing UFF special cases. +129: [12:25:06] UFFTYPER: Unrecognized charge state for atom: 0 +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing Issue239. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing calcEnergy with passed coords. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing calcGrad. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing SFIssue1653802. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing SFIssue2378119. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Test UFF force-field parameter getters. +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing handling missing parameters. +129: [12:25:06] UFFTYPER: Unrecognized hybridization for atom: 0 +129: [12:25:06] UFFTYPER: Unrecognized atom type: Cu+1 (0) +129: [12:25:06] UFFTYPER: Unrecognized hybridization for atom: 0 +129: [12:25:06] UFFTYPER: Unrecognized atom type: Cu+1 (0) +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Testing SFIssue3009337. +129: [12:25:06] done +129: [12:25:06] ------------------------------------- +129: [12:25:06] Test UFF multithreading +129: generating reference data +128: done +128: [12:25:07] done +126: ........ +126: ---------------------------------------------------------------------- +126: Ran 8 tests in 0.091s +126: +126: OK +118/222 Test #128: testMMFFForceFieldHelpersMultiThread ... Passed 0.60 sec test 130 Start 130: testCrystalForceField 130: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField 130: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF 130: Test timeout computed to be: 1500 -119/222 Test #124: pyPartialCharges ....................... Passed 0.35 sec +130: ------------------------------------- +130: Test CrystalFF torsional term. +110: =>start test GETAWAY +110: [12:25:07] test on : 365 molecules done +119/222 Test #110: testGETAWAY ............................ Passed 3.80 sec test 131 Start 131: pyForceFieldHelpers 131: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 131: Test timeout computed to be: 1500 -130: ------------------------------------- -130: Test CrystalFF torsional term. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing UFF special cases. -129: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 0 -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing Issue239. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing calcEnergy with passed coords. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing calcGrad. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing SFIssue1653802. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing SFIssue2378119. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Test UFF force-field parameter getters. -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing handling missing parameters. -129: [03:17:35] UFFTYPER: Unrecognized hybridization for atom: 0 -129: [03:17:35] UFFTYPER: Unrecognized atom type: Cu+1 (0) -129: [03:17:35] UFFTYPER: Unrecognized hybridization for atom: 0 -129: [03:17:35] UFFTYPER: Unrecognized atom type: Cu+1 (0) -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Testing SFIssue3009337. -129: [03:17:35] done -129: [03:17:35] ------------------------------------- -129: [03:17:35] Test UFF multithreading -120/222 Test #130: testCrystalForceField .................. Passed 0.15 sec +120/222 Test #130: testCrystalForceField .................. Passed 0.19 sec test 132 Start 132: testDistGeomHelpers 132: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 132: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 132: Test timeout computed to be: 1500 -129: generating reference data 127: processing 127: launch :0 127: launch :1 127: launch :2 127: launch :3 -127: [03:17:35] Rep: 0 Mol:3 -128: done -128: [03:17:35] done -127: [03:17:35] [03:17:35] Rep: 0 Mol:2 -127: Rep: 0 Mol:1 -127: [03:17:35] Rep: 0 Mol:7 -127: [03:17:35] Rep: 0 Mol:5 -127: [03:17:35] Rep: 0 Mol:11 -127: [03:17:35] Rep: 0 Mol:0 -127: [03:17:35] Rep: 0 Mol:15 -127: [03:17:35] Rep: 0 Mol:19 -127: [03:17:35] Rep: 0 Mol:9 -127: [03:17:35] Rep: 0 Mol:23 -127: [03:17:35] Rep: 0 Mol:27 -127: [03:17:35] Rep: 0 Mol:4 -127: [03:17:35] Rep: 0 Mol:13 -127: [03:17:35] Rep: 0 Mol:31 -132: go -132: ------------------------------------- -132: -127: [03:17:35] Rep: 0 Mol:17 -127: [03:17:35] Rep: 0 Mol:6 -127: [03:17:35] Rep: 0 Mol:10 -127: [03:17:35] Rep: 0 Mol:8 -121/222 Test #128: testMMFFForceFieldHelpersMultiThread ... Passed 0.47 sec +127: [12:25:07] Rep: 0 Mol:3 +121/222 Test #126: pyMolTransforms ........................ Passed 1.21 sec test 133 Start 133: distGeomHelpersCatch 133: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 133: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers 133: Test timeout computed to be: 1500 -126: ........ -126: ---------------------------------------------------------------------- -126: Ran 8 tests in 0.036s -126: -126: OK -127: [03:17:35] Rep: 0 Mol:12 -127: [03:17:35] Rep: 0 Mol:16 -127: [03:17:35] Rep: 0 Mol:21 -127: [03:17:35] Rep: 0 Mol:20 -127: [03:17:35] Rep: 0 Mol:25 -133: Randomness seeded to: 382269401 -127: [03:17:35] Rep: 0 Mol:29 -127: [03:17:35] Rep: 0 Mol:24 -127: [03:17:35] Rep: 20 Mol:3 -127: [03:17:35] Rep: 0 Mol:28 -127: [03:17:35] Rep: 20 Mol:7 -127: [03:17:35] Rep: 20 Mol:11 -127: [03:17:35] Rep: 20 Mol:15 -127: [03:17:35] Rep: 20 Mol:19 -127: [03:17:35] Rep: 0 Mol:14 -127: [03:17:35] Rep: 20 Mol:23 -127: [03:17:35] Rep: 20 Mol:27 -127: [03:17:35] Rep: 20 Mol:31 -127: [03:17:35] Rep: 0 Mol:18 -133: [03:17:35] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] -133: [03:17:35] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] -133: [03:17:35] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] -127: [03:17:35] Rep: 0 Mol:22 -133: [03:17:35] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -122/222 Test #126: pyMolTransforms ........................ Passed 0.60 sec -test 134 - Start 134: pyDistGeomHelpers - -134: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" -134: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap -134: Test timeout computed to be: 1500 -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -133: [03:17:35] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: ----------- -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -133: ----------- -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -133: ----------- -127: [03:17:35] Rep: 0 Mol:26 -133: ----------- -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [03:17:35] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -127: [03:17:35] Rep: 0 Mol:30 -127: [03:17:35] Rep: 40 Mol:3 -127: [03:17:35] Rep: 40 Mol:7 -127: [03:17:35] Rep: 40 Mol:11 -127: [03:17:35] Rep: 40 Mol:15 -127: [03:17:35] Rep: 40 Mol:19 -127: [03:17:35] Rep: 40 Mol:23 -127: [03:17:35] Rep: 40 Mol:27 -127: [03:17:35] Rep: 40 Mol:31 -127: [03:17:35] Rep: 20 Mol:0 -127: [03:17:35] Rep: 20 Mol:1 -133: [03:17:35] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -133: [03:17:35] UFFTYPER: Unrecognized atom type: N_5 (2) -133: [03:17:35] UFFTYPER: Unrecognized atom type: N_5 (3) -133: [03:17:35] UFFTYPER: Unrecognized atom type: N_5 (2) -133: [03:17:35] UFFTYPER: Unrecognized atom type: N_5 (3) -127: [03:17:35] Rep: 20 Mol:4 -133: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 1 -127: [03:17:35] Rep: 20 Mol:5 -127: [03:17:35] Rep: 20 Mol:9 -127: [03:17:35] Rep: 20 Mol:13 -127: [03:17:35] Rep: 20 Mol:17 -127: [03:17:35] Rep: 20 Mol:21 -127: [03:17:35] Rep: 20 Mol:25 -127: [03:17:35] Rep: 20 Mol:29 -133: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 1 -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -133: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 1 -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: ..[03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -127: [03:17:35] Rep: 20 Mol:8 -127: [03:17:35] Rep: 20 Mol:12 -127: [03:17:35] Rep: 20 Mol:16 -127: [03:17:35] Rep: 20 Mol:20 -127: [03:17:35] Rep: 20 Mol:24 -127: [03:17:35] Rep: 20 Mol:28 -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() +127: [12:25:07] Rep: 0 Mol:1 +127: [12:25:07] Rep: 0 Mol:5 +127: [12:25:07] Rep: 0 Mol:0 +127: [12:25:07] Rep: 0 Mol:2 +127: [12:25:07] Rep: 0 Mol:9 +127: [12:25:07] Rep: 0 Mol:4 +127: [12:25:07] Rep: 0 Mol:13 +132: go +132: ------------------------------------- +132: +127: [12:25:07] Rep: 0 Mol:17 +133: Randomness seeded to: 3994274969 +127: [12:25:07] Rep: 0 Mol:6 +127: [12:25:07] Rep: 0 Mol:10 +127: [12:25:07] Rep: 0 Mol:8 +127: [12:25:07] Rep: 0 Mol:7 +127: [12:25:07] Rep: 0 Mol:12 +127: [12:25:07] Rep: 0 Mol:11 +127: [12:25:07] Rep: 0 Mol:15 +127: [12:25:07] Rep: 0 Mol:16 +127: [12:25:07] Rep: 0 Mol:19 +127: [12:25:07] Rep: 0 Mol:21 +127: [12:25:07] Rep: 0 Mol:20 +133: [12:25:07] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] +133: [12:25:07] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +127: [12:25:07] Rep: 0 Mol:23 +127: [12:25:07] Rep: 0 Mol:25 +127: [12:25:07] Rep: 0 Mol:24 +127: [12:25:07] Rep: 0 Mol:27 +127: [12:25:07] Rep: 0 Mol:31 +133: [12:25:07] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] +133: [12:25:07] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +127: [12:25:07] Rep: 0 Mol:29 129: processing 129: launch :0 129: launch :1 129: launch :2 129: launch :3 -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:17:35] Rep: 0 Mol:2 -129: [03:17:35] Rep: 0 Mol:1 -129: [03:17:35] Rep: 0 Mol:5 -129: [03:17:35] Rep: 0 Mol:9 -129: [03:17:35] Rep: 0 Mol:3 -129: [03:17:35] Rep: 0 Mol:0 -129: [03:17:35] Rep: 0 Mol:4 -129: [03:17:35] Rep: 0 Mol:13 -127: [03:17:35] Rep: 60 Mol:3 -127: [03:17:35] Rep: 60 Mol:7 -129: [03:17:35] Rep: 0 Mol:6 -129: [03:17:35] Rep: 0 Mol:10 -129: [03:17:35] Rep: 0 Mol:7 -129: [03:17:35] Rep: 0 Mol:11 -129: [03:17:35] Rep: 0 Mol:17 -129: [03:17:35] Rep: 0 Mol:15 -129: [03:17:35] Rep: 0 Mol:19 -127: [03:17:35] Rep: 60 Mol:11 -127: [03:17:35] Rep: 60 Mol:15 -127: [03:17:35] Rep: 60 Mol:19 -127: [03:17:35] Rep: 60 Mol:23 -127: [03:17:35] Rep: 60 Mol:27 -127: [03:17:35] Rep: 60 Mol:31 -133: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 5 -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -133: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 5 -129: [03:17:35] Rep: 0 Mol:23 -129: [03:17:35] Rep: 0 Mol:27 -129: [03:17:35] Rep: 0 Mol:31 -133: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 5 -129: [03:17:35] Rep: 0 Mol:8 -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:17:35] Rep: 0 Mol:12 -129: [03:17:35] Rep: 0 Mol:16 -129: [03:17:35] Rep: 0 Mol:21 -129: [03:17:35] Rep: 0 Mol:20 -129: [03:17:35] Rep: 0 Mol:25 -129: [03:17:35] Rep: 0 Mol:14 -129: [03:17:35] Rep: 0 Mol:18 -129: [03:17:35] Rep: 0 Mol:24 -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[03:17:35] UFFTYPER: Unrecognized hybridization for atom: 0 -131: [03:17:35] UFFTYPER: Unrecognized atom type: Cu+1 (0) -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -129: [03:17:35] Rep: 0 Mol:29 -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[03:17:35] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: .[03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: ..[03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:17:35] Rep: 0 Mol:22 -129: [03:17:35] Rep: 0 Mol:28 -131: [03:17:35] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:17:35] Rep: 0 Mol:26 -133: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 6 -129: [03:17:35] Rep: 0 Mol:30 -133: [03:17:35] UFFTYPER: Unrecognized charge state for atom: 6 -133: [03:17:36] UFFTYPER: Unrecognized charge state for atom: 6 -127: [03:17:36] Rep: 40 Mol:1 -127: [03:17:36] Rep: 40 Mol:5 -127: [03:17:36] Rep: 40 Mol:9 -127: [03:17:36] Rep: 40 Mol:13 -127: [03:17:36] Rep: 40 Mol:17 -127: [03:17:36] Rep: 40 Mol:21 -127: [03:17:36] Rep: 40 Mol:25 -127: [03:17:36] Rep: 40 Mol:29 +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +133: [12:25:07] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +127: [12:25:07] Rep: 0 Mol:28 +129: [12:25:07] Rep: 0 Mol:1 +129: [12:25:07] Rep: 0 Mol:5 +129: [12:25:07] Rep: 0 Mol:9 +129: [12:25:07] Rep: 0 Mol:3 +133: ----------- +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [12:25:07] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +129: [12:25:07] Rep: 0 Mol:0 +129: [12:25:07] Rep: 0 Mol:2 +129: [12:25:07] Rep: 0 Mol:13 +129: [12:25:07] Rep: 0 Mol:4 +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +133: ----------- +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +127: [12:25:07] Rep: 0 Mol:14 +129: [12:25:07] Rep: 0 Mol:17 +133: [12:25:07] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +133: ----------- +129: [12:25:07] Rep: 0 Mol:7 +129: [12:25:07] Rep: 0 Mol:11 +129: [12:25:07] Rep: 0 Mol:15 +133: ----------- +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [12:25:07] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +129: [12:25:07] Rep: 0 Mol:6 +129: [12:25:07] Rep: 0 Mol:10 +127: [12:25:07] Rep: 0 Mol:18 +129: [12:25:07] Rep: 0 Mol:8 +129: [12:25:07] Rep: 0 Mol:21 +129: [12:25:07] Rep: 0 Mol:19 +129: [12:25:07] Rep: 0 Mol:23 +129: [12:25:07] Rep: 0 Mol:27 +127: [12:25:07] Rep: 0 Mol:22 +129: [12:25:07] Rep: 0 Mol:12 +129: [12:25:07] Rep: 0 Mol:25 +129: [12:25:07] Rep: 0 Mol:16 +129: [12:25:07] Rep: 0 Mol:31 +129: [12:25:07] Rep: 0 Mol:20 +129: [12:25:07] Rep: 0 Mol:29 +129: [12:25:07] Rep: 0 Mol:14 +127: [12:25:07] Rep: 0 Mol:26 +129: [12:25:07] Rep: 0 Mol:24 +129: [12:25:07] Rep: 0 Mol:28 +129: [12:25:07] Rep: 0 Mol:18 +127: [12:25:07] Rep: 0 Mol:30 +129: [12:25:07] Rep: 0 Mol:22 +129: [12:25:07] Rep: 0 Mol:26 +129: [12:25:07] Rep: 0 Mol:30 +127: [12:25:07] Rep: 20 Mol:3 +127: [12:25:07] Rep: 20 Mol:7 +127: [12:25:07] Rep: 20 Mol:11 +127: [12:25:07] Rep: 20 Mol:15 +127: [12:25:07] Rep: 20 Mol:19 +127: [12:25:07] Rep: 20 Mol:23 +127: [12:25:07] Rep: 20 Mol:27 +133: [12:25:07] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +133: [12:25:07] UFFTYPER: Unrecognized atom type: N_5 (2) +133: [12:25:07] UFFTYPER: Unrecognized atom type: N_5 (3) +133: [12:25:07] UFFTYPER: Unrecognized atom type: N_5 (2) +133: [12:25:07] UFFTYPER: Unrecognized atom type: N_5 (3) +127: [12:25:07] Rep: 20 Mol:31 +133: [12:25:07] UFFTYPER: Unrecognized charge state for atom: 1 +133: [12:25:07] UFFTYPER: Unrecognized charge state for atom: 1 +127: [12:25:07] Rep: 20 Mol:1 +127: [12:25:07] Rep: 20 Mol:5 +127: [12:25:07] Rep: 20 Mol:9 +127: [12:25:07] Rep: 20 Mol:13 +127: [12:25:07] Rep: 20 Mol:17 +127: [12:25:07] Rep: 20 Mol:21 +127: [12:25:07] Rep: 20 Mol:25 +127: [12:25:07] Rep: 20 Mol:29 +127: [12:25:07] Rep: 20 Mol:0 +127: [12:25:07] Rep: 20 Mol:4 +127: [12:25:07] Rep: 20 Mol:8 +127: [12:25:07] Rep: 20 Mol:12 +127: [12:25:07] Rep: 20 Mol:16 +127: [12:25:07] Rep: 20 Mol:20 +127: [12:25:07] Rep: 20 Mol:24 +127: [12:25:07] Rep: 20 Mol:28 +133: [12:25:07] UFFTYPER: Unrecognized charge state for atom: 1 +127: [12:25:08] Rep: 40 Mol:3 +127: [12:25:08] Rep: 40 Mol:7 +133: [12:25:08] UFFTYPER: Unrecognized charge state for atom: 5 +127: [12:25:08] Rep: 40 Mol:11 +127: [12:25:08] Rep: 40 Mol:15 +127: [12:25:08] Rep: 40 Mol:19 +127: [12:25:08] Rep: 40 Mol:23 +127: [12:25:08] Rep: 40 Mol:27 +127: [12:25:08] Rep: 40 Mol:31 +133: [12:25:08] UFFTYPER: Unrecognized charge state for atom: 5 +133: [12:25:08] UFFTYPER: Unrecognized charge state for atom: 5 +127: [12:25:08] Rep: 40 Mol:0 +127: [12:25:08] Rep: 40 Mol:4 +127: [12:25:08] Rep: 40 Mol:8 +127: [12:25:08] Rep: 40 Mol:12 +127: [12:25:08] Rep: 40 Mol:16 +127: [12:25:08] Rep: 40 Mol:20 +127: [12:25:08] Rep: 40 Mol:24 +127: [12:25:08] Rep: 40 Mol:28 +127: [12:25:08] Rep: 40 Mol:1 +127: [12:25:08] Rep: 40 Mol:5 +127: [12:25:08] Rep: 40 Mol:9 +127: [12:25:08] Rep: 40 Mol:13 +127: [12:25:08] Rep: 40 Mol:17 +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +127: [12:25:08] Rep: 40 Mol:21 +127: [12:25:08] Rep: 40 Mol:25 +127: [12:25:08] Rep: 40 Mol:29 +127: [12:25:08] Rep: 20 Mol:2 +127: [12:25:08] Rep: 20 Mol:6 +127: [12:25:08] Rep: 20 Mol:10 +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: ..[12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +133: [12:25:08] UFFTYPER: Unrecognized charge state for atom: 6 +127: [12:25:08] Rep: 20 Mol:14 +127: [12:25:08] Rep: 20 Mol:18 +127: [12:25:08] Rep: 20 Mol:22 +127: [12:25:08] Rep: 20 Mol:26 +127: [12:25:08] Rep: 20 Mol:30 +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +133: [12:25:08] UFFTYPER: Unrecognized charge state for atom: 6 +133: [12:25:08] UFFTYPER: Unrecognized charge state for atom: 6 +127: [12:25:08] Rep: 60 Mol:3 +127: [12:25:08] Rep: 60 Mol:7 +127: [12:25:08] Rep: 60 Mol:11 +127: [12:25:08] Rep: 60 Mol:15 +127: [12:25:08] Rep: 60 Mol:19 +127: [12:25:08] Rep: 60 Mol:23 +127: [12:25:08] Rep: 60 Mol:27 +127: [12:25:08] Rep: 60 Mol:31 +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:25:08] Rep: 100 Mol:3 +129: [12:25:08] Rep: 100 Mol:7 +129: [12:25:08] Rep: 100 Mol:11 +129: [12:25:08] Rep: 100 Mol:15 +129: [12:25:08] Rep: 100 Mol:19 +129: [12:25:08] Rep: 100 Mol:23 +129: [12:25:08] Rep: 100 Mol:27 +129: [12:25:08] Rep: 100 Mol:31 +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:25:08] UFFTYPER: Unrecognized hybridization for atom: 0 +131: [12:25:08] UFFTYPER: Unrecognized atom type: Cu+1 (0) +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:25:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: .[12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: ..[12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +127: [12:25:08] Rep: 60 Mol:0 +127: [12:25:08] Rep: 60 Mol:4 +127: [12:25:08] Rep: 60 Mol:8 +127: [12:25:08] Rep: 60 Mol:12 +127: [12:25:08] Rep: 60 Mol:16 +127: [12:25:08] Rep: 60 Mol:20 +127: [12:25:08] Rep: 60 Mol:24 +127: [12:25:08] Rep: 60 Mol:28 +131: [12:25:08] Molecule does not have explicit Hs. Consider calling AddHs() +127: [12:25:08] Rep: 80 Mol:3 +127: [12:25:08] Rep: 80 Mol:7 +127: [12:25:08] Rep: 80 Mol:11 +127: [12:25:08] Rep: 80 Mol:15 +127: [12:25:08] Rep: 80 Mol:19 +127: [12:25:08] Rep: 80 Mol:23 +127: [12:25:08] Rep: 80 Mol:27 +127: [12:25:08] Rep: 80 Mol:31 +127: [12:25:08] Rep: 60 Mol:1 +127: [12:25:08] Rep: 60 Mol:5 +127: [12:25:08] Rep: 60 Mol:9 +127: [12:25:08] Rep: 60 Mol:13 +127: [12:25:08] Rep: 60 Mol:17 +127: [12:25:08] Rep: 60 Mol:21 +127: [12:25:08] Rep: 60 Mol:25 +127: [12:25:08] Rep: 60 Mol:29 +129: [12:25:08] Rep: 100 Mol:1 +129: [12:25:08] Rep: 100 Mol:5 +129: [12:25:08] Rep: 100 Mol:9 +129: [12:25:08] Rep: 100 Mol:13 +129: [12:25:08] Rep: 100 Mol:17 +129: [12:25:08] Rep: 100 Mol:21 +129: [12:25:08] Rep: 100 Mol:25 +129: [12:25:08] Rep: 100 Mol:29 +129: [12:25:08] Rep: 100 Mol:0 +129: [12:25:08] Rep: 100 Mol:4 +129: [12:25:08] Rep: 100 Mol:8 +129: [12:25:08] Rep: 100 Mol:12 +129: [12:25:08] Rep: 100 Mol:16 131: ... 131: ---------------------------------------------------------------------- -131: Ran 18 tests in 0.176s +131: Ran 18 tests in 0.400s 131: 131: OK -134: .[03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -127: [03:17:36] Rep: 20 Mol:2 -127: [03:17:36] Rep: 20 Mol:6 -127: [03:17:36] Rep: 80 Mol:3 -127: [03:17:36] Rep: 80 Mol:7 -127: [03:17:36] Rep: 80 Mol:11 -127: [03:17:36] Rep: 80 Mol:15 -127: [03:17:36] Rep: 80 Mol:19 -127: [03:17:36] Rep: 80 Mol:23 -127: [03:17:36] Rep: 80 Mol:27 -127: [03:17:36] Rep: 80 Mol:31 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: ..[03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -127: [03:17:36] Rep: 20 Mol:10 -127: [03:17:36] Rep: 20 Mol:14 -127: [03:17:36] Rep: 20 Mol:18 -127: [03:17:36] Rep: 20 Mol:22 -127: [03:17:36] Rep: 20 Mol:26 -127: [03:17:36] Rep: 20 Mol:30 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: ..[03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: .[03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -127: [03:17:36] Rep: 40 Mol:0 -127: [03:17:36] Rep: 40 Mol:4 -127: [03:17:36] Rep: 40 Mol:8 -127: [03:17:36] Rep: 40 Mol:12 -127: [03:17:36] Rep: 40 Mol:16 -127: [03:17:36] Rep: 40 Mol:20 -127: [03:17:36] Rep: 40 Mol:24 -127: [03:17:36] Rep: 40 Mol:28 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -123/222 Test #131: pyForceFieldHelpers .................... Passed 0.71 sec +129: [12:25:08] Rep: 100 Mol:20 +129: [12:25:08] Rep: 100 Mol:24 +129: [12:25:08] Rep: 100 Mol:28 +127: [12:25:08] Rep: 40 Mol:2 +127: [12:25:08] Rep: 40 Mol:6 +127: [12:25:08] Rep: 40 Mol:10 +127: [12:25:08] Rep: 40 Mol:14 +127: [12:25:08] Rep: 40 Mol:18 +127: [12:25:08] Rep: 40 Mol:22 +127: [12:25:08] Rep: 40 Mol:26 +127: [12:25:08] Rep: 40 Mol:30 +127: [12:25:08] Rep: 80 Mol:0 +127: [12:25:08] Rep: 80 Mol:4 +127: [12:25:08] Rep: 80 Mol:8 +127: [12:25:08] Rep: 80 Mol:12 +127: [12:25:08] Rep: 80 Mol:16 +127: [12:25:08] Rep: 80 Mol:20 +127: [12:25:08] Rep: 80 Mol:24 +127: [12:25:08] Rep: 80 Mol:28 +127: [12:25:08] Rep: 80 Mol:1 +122/222 Test #131: pyForceFieldHelpers .................... Passed 1.61 sec +test 134 + Start 134: pyDistGeomHelpers + +134: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" +134: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap +134: Test timeout computed to be: 1500 +127: [12:25:08] Rep: 80 Mol:5 +127: [12:25:08] Rep: 80 Mol:9 +127: [12:25:08] Rep: 80 Mol:13 +127: [12:25:08] Rep: 80 Mol:17 +127: [12:25:08] Rep: 80 Mol:21 +127: [12:25:08] Rep: 80 Mol:25 +127: [12:25:08] Rep: 80 Mol:29 +129: [12:25:09] Rep: 100 Mol:2 +129: [12:25:09] Rep: 100 Mol:6 +129: [12:25:09] Rep: 100 Mol:10 +129: [12:25:09] Rep: 100 Mol:14 +129: [12:25:09] Rep: 100 Mol:18 +129: [12:25:09] Rep: 100 Mol:22 +129: [12:25:09] Rep: 100 Mol:26 +129: [12:25:09] Rep: 100 Mol:30 +127: [12:25:09] Rep: 60 Mol:2 +127: [12:25:09] Rep: 60 Mol:6 +127: [12:25:09] Rep: 60 Mol:10 +127: [12:25:09] Rep: 60 Mol:14 +127: [12:25:09] Rep: 60 Mol:18 +127: [12:25:09] Rep: 60 Mol:22 +127: [12:25:09] Rep: 60 Mol:26 +127: [12:25:09] Rep: 60 Mol:30 +134: .[12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: ..[12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +127: [12:25:09] Rep: 80 Mol:2 +127: [12:25:09] Rep: 80 Mol:6 +127: [12:25:09] Rep: 80 Mol:10 +127: [12:25:09] Rep: 80 Mol:14 +127: [12:25:09] Rep: 80 Mol:18 +127: [12:25:09] Rep: 80 Mol:22 +127: [12:25:09] Rep: 80 Mol:26 +127: [12:25:09] Rep: 80 Mol:30 +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: ..[12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: .[12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +105: =>start test GETAWAY custom +105: [12:25:09] test on : 365 molecules done +123/222 Test #105: testRDFcustom .......................... Passed 8.30 sec test 135 Start 135: testMolAlign 135: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 135: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 135: Test timeout computed to be: 1500 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -127: [03:17:36] Rep: 60 Mol:1 -127: [03:17:36] Rep: 60 Mol:5 -127: [03:17:36] Rep: 60 Mol:9 -127: [03:17:36] Rep: 60 Mol:13 -127: [03:17:36] Rep: 60 Mol:17 -127: [03:17:36] Rep: 60 Mol:21 -127: [03:17:36] Rep: 60 Mol:25 -127: [03:17:36] Rep: 60 Mol:29 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -127: [03:17:36] Rep: 60 Mol:0 -127: [03:17:36] Rep: 60 Mol:4 -127: [03:17:36] Rep: 60 Mol:8 -127: [03:17:36] Rep: 60 Mol:12 -127: [03:17:36] Rep: 60 Mol:16 -127: [03:17:36] Rep: 60 Mol:20 -127: [03:17:36] Rep: 60 Mol:24 -127: [03:17:36] Rep: 60 Mol:28 -127: [03:17:36] Rep: 80 Mol:1 -127: [03:17:36] Rep: 80 Mol:5 -127: [03:17:36] Rep: 80 Mol:9 -127: [03:17:36] Rep: 80 Mol:13 -127: [03:17:36] Rep: 80 Mol:17 -127: [03:17:36] Rep: 80 Mol:21 -127: [03:17:36] Rep: 80 Mol:25 -127: [03:17:36] Rep: 80 Mol:29 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -127: [03:17:36] Rep: 40 Mol:2 -127: [03:17:36] Rep: 40 Mol:6 -127: [03:17:36] Rep: 40 Mol:10 -127: [03:17:36] Rep: 40 Mol:14 -127: [03:17:36] Rep: 40 Mol:18 -127: [03:17:36] Rep: 40 Mol:22 -127: [03:17:36] Rep: 40 Mol:26 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:25:09] done +129: [12:25:09] ------------------------------------- +129: [12:25:09] Test UFF multithreading2 +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:09] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +127: [12:25:10] done +127: [12:25:10] ------------------------------------- +127: [12:25:10] Test MMFF multithreading2 135: *********************************************************** 135: Testing MolAlign 135: --------------------------------- @@ -19537,149 +19616,115 @@ 135: testIssue241 135: 135: *********************************************************** -124/222 Test #135: testMolAlign ........................... Passed 0.15 sec +124/222 Test #135: testMolAlign ........................... Passed 0.40 sec test 136 Start 136: testO3AAlign 136: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 136: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 136: Test timeout computed to be: 1500 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -134: .[03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -127: [03:17:36] Rep: 40 Mol:30 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:17:36] Rep: 100 Mol:3 -129: [03:17:36] Rep: 100 Mol:7 -129: [03:17:36] Rep: 100 Mol:11 -129: [03:17:36] Rep: 100 Mol:15 -129: [03:17:36] Rep: 100 Mol:19 -129: [03:17:36] Rep: 100 Mol:23 -129: [03:17:36] Rep: 100 Mol:27 -129: [03:17:36] Rep: 100 Mol:31 -63: [03:17:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -63: [03:17:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -127: [03:17:36] Rep: 80 Mol:0 -127: [03:17:36] Rep: 80 Mol:4 -127: [03:17:36] Rep: 80 Mol:8 -127: [03:17:36] Rep: 80 Mol:12 -127: [03:17:36] Rep: 80 Mol:16 -127: [03:17:36] Rep: 80 Mol:20 -127: [03:17:36] Rep: 80 Mol:24 -127: [03:17:36] Rep: 80 Mol:28 -127: [03:17:36] Rep: 60 Mol:2 -127: [03:17:36] Rep: 60 Mol:6 -127: [03:17:36] Rep: 60 Mol:10 -127: [03:17:36] Rep: 60 Mol:14 -127: [03:17:36] Rep: 60 Mol:18 -127: [03:17:36] Rep: 60 Mol:22 -127: [03:17:36] Rep: 60 Mol:26 -127: [03:17:36] Rep: 60 Mol:30 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -63: ---------------------------------- -63: ---------------------------------- -63: [03:17:36] -63: -63: **** -63: Pre-condition Violation -63: rlabel out of range for MDL files -63: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp -63: Failed Expression: rlabel >= 0 && rlabel < 100 -63: **** -63: -63: [03:17:36] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -129: [03:17:36] Rep: 100 Mol:0 -129: [03:17:36] Rep: 100 Mol:4 -129: [03:17:36] Rep: 100 Mol:8 -129: [03:17:36] Rep: 100 Mol:12 -129: [03:17:36] Rep: 100 Mol:16 -129: [03:17:36] Rep: 100 Mol:20 -129: [03:17:36] Rep: 100 Mol:24 -129: [03:17:36] Rep: 100 Mol:28 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -127: [03:17:36] Rep: 80 Mol:2 -127: [03:17:36] Rep: 80 Mol:6 -127: [03:17:36] Rep: 80 Mol:10 -127: [03:17:36] Rep: 80 Mol:14 -127: [03:17:36] Rep: 80 Mol:18 -127: [03:17:36] Rep: 80 Mol:22 -127: [03:17:36] Rep: 80 Mol:26 -129: [03:17:36] Rep: 100 Mol:1 -129: [03:17:36] Rep: 100 Mol:5 -129: [03:17:36] Rep: 100 Mol:9 -129: [03:17:36] Rep: 100 Mol:13 -129: [03:17:36] Rep: 100 Mol:17 -129: [03:17:36] Rep: 100 Mol:21 -129: [03:17:36] Rep: 100 Mol:25 -129: [03:17:36] Rep: 100 Mol:29 -127: [03:17:36] Rep: 80 Mol:30 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -63: [03:17:36] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -63: [03:17:36] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -63: [03:17:36] Empty atom list: 'M ALS 1 0 F' on line 8. -125/222 Test #63: fileParsersTest1 ....................... Passed 7.08 sec +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +133: [12:25:10] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +133: [12:25:10] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +133: [12:25:10] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +133: [12:25:10] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +133: [12:25:10] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +134: [12:25:10] Molecule does not have explicit Hs. Consider calling AddHs() +133: [12:25:10] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +134: .[12:25:11] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:25:11] done +129: [12:25:11] ------------------------------------- +129: [12:25:11] Test UFF multithreading3 +127: [12:25:11] done +127: [12:25:11] ------------------------------------- +127: [12:25:11] Test MMFF multithreading3 +134: [12:25:11] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:25:12] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:25:12] done +129: [12:25:12] ------------------------------------- +129: [12:25:12] Testing GitHubIssue62. +129: [12:25:12] beta-lactam 39.6387 +129: [12:25:12] cyclopropanone 174.698 +129: [12:25:12] aziridine 337.986 +129: [12:25:12] aziridinone 115.248 +129: [12:25:12] isobutene 2.48217 +129: [12:25:12] acetone 1.91788 +129: [12:25:12] cyclopentanone 10.1648 +129: [12:25:12] cyclopropene 99.4921 +129: [12:25:12] cyclobutene 41.0156 +129: [12:25:12] cyclopropane 267.236 +129: [12:25:12] gamma-lactam 15.7471 +129: [12:25:12] trans-2,3-diphenylcyclopropan-1-one 203.398 +132: building molecules +127: [12:25:12] done +127: [12:25:12] ------------------------------------- +127: [12:25:12] Testing github 162: Incorrect SMILES after MMFF parameterization . +127: [12:25:12] done +127: [12:25:12] ------------------------------------- +127: [12:25:12] Testing github 224: crash during MMFF parameterization . +127: [12:25:12] done +127: [12:25:12] ------------------------------------- +127: [12:25:12] Testing github6728: crash due to missing stretch-bend params. +132: generating reference data +125/222 Test #127: testMMFFForceFieldHelpers .............. Passed 6.00 sec test 137 Start 137: molAlignCatchTest 137: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 137: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign 137: Test timeout computed to be: 1500 -127: [03:17:36] done -127: [03:17:36] ------------------------------------- -127: [03:17:36] Test MMFF multithreading2 -133: [03:17:36] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -134: [03:17:36] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:17:37] Rep: 100 Mol:2 -129: [03:17:37] Rep: 100 Mol:6 -129: [03:17:37] Rep: 100 Mol:10 -129: [03:17:37] Rep: 100 Mol:14 -129: [03:17:37] Rep: 100 Mol:18 -129: [03:17:37] Rep: 100 Mol:22 -129: [03:17:37] Rep: 100 Mol:26 -129: [03:17:37] Rep: 100 Mol:30 -133: [03:17:37] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -133: [03:17:37] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -137: Randomness seeded to: 2493838165 -137: 128374726 -133: [03:17:37] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -133: [03:17:37] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -133: [03:17:37] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -137: 137271456 -83: 0,0 0 -83: 0,1 0 -83: 1,0 0 -83: 1,1 0 -83: 2,0 0 -83: 2,1 0 -126/222 Test #83: testEnumeration ........................ Passed 6.64 sec +134: [12:25:12] Molecule does not have explicit Hs. Consider calling AddHs() +129: [12:25:12] cis-2,3-diphenylcyclopropan-1-one 206.852 +137: Randomness seeded to: 978632156 +137: 85565480 +129: [12:25:12] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +129: [12:25:12] cyclopropylidencyclobutane 218.879 +137: 75946120 +129: [12:25:12] diphenylmethylidencyclobutane 79.6139 +129: [12:25:12] done +129: [12:25:12] ------------------------------------- +129: [12:25:12] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +129: [12:25:12] done +129: [12:25:12] ------------------------------------- +129: [12:25:12] Test square planar complexes +129: [12:25:12] done +129: [12:25:12] ------------------------------------- +129: [12:25:12] Test octahedral complexes +129: [12:25:12] done +126/222 Test #129: testUFFForceFieldHelpers ............... Passed 6.26 sec test 138 Start 138: pyMolAlign 138: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 138: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolAlign/Wrap 138: Test timeout computed to be: 1500 -127: [03:17:37] done -127: [03:17:37] ------------------------------------- -127: [03:17:37] Test MMFF multithreading3 -129: [03:17:37] done -129: [03:17:37] ------------------------------------- -129: [03:17:37] Test UFF multithreading2 -116: [03:17:37] done -116: [03:17:37] ------------------------------------- -116: [03:17:37] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Test unfolded version of RDKFP -116: [03:17:38] ------------------------------------- -116: [03:17:38] Test bitinfo of RDKFP +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Test unfolded version of RDKFP +116: [12:25:12] ------------------------------------- +116: [12:25:12] Test bitinfo of RDKFP 116: 562: [ 2 ], 116: 709: [ 0 1 ], 116: 1118: [ 0 1 2 ], @@ -19691,86 +19736,86 @@ 116: 1772: [ 0 ], [ 1 ], 116: 1813: [ 0 1 ], 116: ------------ -116: [03:17:38] ------------------------------------- -116: [03:17:38] Single atoms setting radius 1 bits in Morgan fingerprints -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Github #879: Pattern fingerprint should set bits for single-atom fragments. -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Github #2115: BitInfo not complete for RDKFingerprint -116: [03:17:38] done -116: [03:17:38] ------------------------------------- -116: [03:17:38] Github #3723: Fingerprint crash for mols with Zero order bonds -116: [03:17:38] done -127/222 Test #116: testFingerprints ....................... Passed 3.98 sec +116: [12:25:12] ------------------------------------- +116: [12:25:12] Single atoms setting radius 1 bits in Morgan fingerprints +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Github #879: Pattern fingerprint should set bits for single-atom fragments. +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Github #2115: BitInfo not complete for RDKFingerprint +116: [12:25:12] done +116: [12:25:12] ------------------------------------- +116: [12:25:12] Github #3723: Fingerprint crash for mols with Zero order bonds +116: [12:25:12] done +127/222 Test #116: testFingerprints ....................... Passed 8.74 sec test 139 Start 139: testFeatures 139: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 139: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures 139: Test timeout computed to be: 1500 -139: [03:17:38] ------------------------------------- -139: [03:17:38] AtomType parser testing. -139: [03:17:38] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -139: [03:17:38] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] FeatureDefinition parser testing. -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Test pulling feat defs from a string. -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] FeatureDef functionality testing. -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] FeatureFactory testing. -139: [03:17:38] 1 -139: [03:17:38] 2 -139: [03:17:38] 3 -139: [03:17:38] 4 -139: [03:17:38] 5 -139: [03:17:38] 6 -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Feature Location testing. -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Test building a FeatureFactory from a file -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Testing Issue 224. -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Testing Issue 225. -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Test Issue346 -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Test Issue347 -139: [03:17:38] done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Testing Issue 348. -139: [03:17:38] SMARTS Parse Error: syntax error while parsing: [C[C] -139: [03:17:38] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -139: [03:17:38] ------------------------------------- -139: [03:17:38] Testing Nested AtomType definitions. +139: [12:25:12] ------------------------------------- +139: [12:25:12] AtomType parser testing. +139: [12:25:12] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +139: [12:25:12] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] FeatureDefinition parser testing. +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Test pulling feat defs from a string. +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] FeatureDef functionality testing. +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] FeatureFactory testing. +139: [12:25:12] 1 +139: [12:25:12] 2 +139: [12:25:12] 3 +139: [12:25:12] 4 +139: [12:25:12] 5 +139: [12:25:12] 6 +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Feature Location testing. +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Test building a FeatureFactory from a file +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Testing Issue 224. +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Testing Issue 225. +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Test Issue346 +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Test Issue347 +139: [12:25:12] done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Testing Issue 348. +139: [12:25:12] SMARTS Parse Error: syntax error while parsing: [C[C] +139: [12:25:12] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +139: [12:25:12] ------------------------------------- +139: [12:25:12] Testing Nested AtomType definitions. 139: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -139: [03:17:38] ------------------------------------- -139: [03:17:38] Testing Github Issue #252: crash when calling getPos() with no conformer. -139: [03:17:38] expect a precondition failure message below -139: [03:17:38] +139: [12:25:12] ------------------------------------- +139: [12:25:12] Testing Github Issue #252: crash when calling getPos() with no conformer. +139: [12:25:12] expect a precondition failure message below +139: [12:25:12] 139: 139: **** 139: Pre-condition Violation @@ -19779,10 +19824,10 @@ 139: Failed Expression: dp_mol->getNumConformers() 139: **** 139: -139: [03:17:38] Done -139: [03:17:38] ------------------------------------- -139: [03:17:38] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -139: [03:17:38] done +139: [12:25:12] Done +139: [12:25:12] ------------------------------------- +139: [12:25:12] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +139: [12:25:12] done 128/222 Test #139: testFeatures ........................... Passed 0.06 sec test 140 Start 140: pyChemicalFeatures @@ -19790,16 +19835,27 @@ 140: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 140: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 140: Test timeout computed to be: 1500 -127: [03:17:38] done -127: [03:17:38] ------------------------------------- -127: [03:17:38] Testing github 162: Incorrect SMILES after MMFF parameterization . -127: [03:17:38] done -127: [03:17:38] ------------------------------------- -127: [03:17:38] Testing github 224: crash during MMFF parameterization . -127: [03:17:38] done -127: [03:17:38] ------------------------------------- -127: [03:17:38] Testing github6728: crash due to missing stretch-bend params. -129/222 Test #127: testMMFFForceFieldHelpers .............. Passed 3.14 sec +134: [12:25:13] Molecule does not have explicit Hs. Consider calling AddHs() +63: [12:25:13] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +63: [12:25:13] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +134: [12:25:13] Molecule does not have explicit Hs. Consider calling AddHs() +63: ---------------------------------- +63: ---------------------------------- +63: [12:25:13] +63: +63: **** +63: Pre-condition Violation +63: rlabel out of range for MDL files +63: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp +63: Failed Expression: rlabel >= 0 && rlabel < 100 +63: **** +63: +63: [12:25:13] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +137: 1023358800 +63: [12:25:13] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +63: [12:25:13] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +63: [12:25:13] Empty atom list: 'M ALS 1 0 F' on line 8. +129/222 Test #63: fileParsersTest1 ....................... Passed 18.83 sec test 141 Start 141: testShapeHelpers @@ -19818,39 +19874,27 @@ 141: testGithub4364 141: 141: *********************************************************** -130/222 Test #141: testShapeHelpers ....................... Passed 0.06 sec +130/222 Test #141: testShapeHelpers ....................... Passed 0.02 sec test 142 Start 142: pyShapeHelpers 142: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 142: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 142: Test timeout computed to be: 1500 -134: [03:17:38] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:17:38] done -129: [03:17:38] ------------------------------------- -129: [03:17:38] Test UFF multithreading3 -132: building molecules -132: generating reference data -134: [03:17:38] Molecule does not have explicit Hs. Consider calling AddHs() -140: .[03:17:38] Molecule does not have explicit Hs. Consider calling AddHs() -140: .[03:17:38] Molecule does not have explicit Hs. Consider calling AddHs() -140: ..[03:17:38] Molecule does not have explicit Hs. Consider calling AddHs() -140: .[03:17:38] Molecule does not have explicit Hs. Consider calling AddHs() -140: .[03:17:38] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] -140: [03:17:38] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' -140: ... -140: ---------------------------------------------------------------------- -140: Ran 9 tests in 0.053s -140: -140: OK -131/222 Test #140: pyChemicalFeatures ..................... Passed 0.68 sec +25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +142: . +142: ---------------------------------------------------------------------- +142: Ran 1 test in 0.049s +142: +142: OK +142: Testing Shape Helpers wrapper +131/222 Test #142: pyShapeHelpers ......................... Passed 0.39 sec test 143 Start 143: testMolCatalog 143: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 143: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog 143: Test timeout computed to be: 1500 -134: [03:17:38] Molecule does not have explicit Hs. Consider calling AddHs() 132/222 Test #143: testMolCatalog ......................... Passed 0.03 sec test 144 Start 144: pyMolCatalog @@ -19858,83 +19902,55 @@ 144: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 144: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolCatalog/Wrap 144: Test timeout computed to be: 1500 -134: [03:17:38] Molecule does not have explicit Hs. Consider calling AddHs() -142: . -142: ---------------------------------------------------------------------- -142: Ran 1 test in 0.082s -142: -142: OK -142: Testing Shape Helpers wrapper -134: [03:17:39] Molecule does not have explicit Hs. Consider calling AddHs() -129: [03:17:39] done -129: [03:17:39] ------------------------------------- -129: [03:17:39] Testing GitHubIssue62. -129: [03:17:39] beta-lactam 39.6387 -129: [03:17:39] cyclopropanone 174.698 -129: [03:17:39] aziridine 337.986 -129: [03:17:39] aziridinone 115.248 -129: [03:17:39] isobutene 2.48217 -129: [03:17:39] acetone 1.91788 -129: [03:17:39] cyclopentanone 10.1648 -129: [03:17:39] cyclopropene 99.4921 -129: [03:17:39] cyclobutene 41.0156 -129: [03:17:39] cyclopropane 267.236 -129: [03:17:39] gamma-lactam 15.7471 -133/222 Test #142: pyShapeHelpers ......................... Passed 0.75 sec +140: .[12:25:14] Molecule does not have explicit Hs. Consider calling AddHs() +140: .[12:25:14] Molecule does not have explicit Hs. Consider calling AddHs() +25: All 191 tests passed +137: 744312080 +137: =============================================================================== +137: All tests passed (73 assertions in 3 test cases) +137: +140: ..[12:25:14] Molecule does not have explicit Hs. Consider calling AddHs() +140: .[12:25:14] Molecule does not have explicit Hs. Consider calling AddHs() +140: .[12:25:14] SMARTS Parse Error: syntax error while parsing: [N,O;!HQ] +140: [12:25:14] SMARTS Parse Error: Failed parsing SMARTS '[N,O;!HQ]' for input: '[N,O;!HQ]' +140: ... +140: ---------------------------------------------------------------------- +140: Ran 9 tests in 0.325s +140: +140: OK +133/222 Test #137: molAlignCatchTest ...................... Passed 2.17 sec test 145 Start 145: moldraw2DTest1 145: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 145: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D 145: Test timeout computed to be: 1500 -129: [03:17:39] trans-2,3-diphenylcyclopropan-1-one 203.398 145: ----------------- Test 1 +145: file test1_6.svg gave hash 1109656969U not the expected 2635907956U +145: Done +145: ----------------- Test 2 144: . 144: ---------------------------------------------------------------------- -144: Ran 1 test in 0.006s +144: Ran 1 test in 0.026s 144: 144: OK -129: [03:17:39] cis-2,3-diphenylcyclopropan-1-one 206.852 -145: file test1_6.svg gave hash 1109656969U not the expected 2635907956U -145: Done -145: ----------------- Test 2 -134: [03:17:39] Molecule does not have explicit Hs. Consider calling AddHs() +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 145: file test2_1.png gave hash 3662870653U not the expected 307437906U -137: 1828164253 -129: [03:17:39] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 145: file test2_2.png gave hash 3839236620U not the expected 610424244U -129: [03:17:39] cyclopropylidencyclobutane 218.879 -134/222 Test #144: pyMolCatalog ........................... Passed 0.38 sec -test 146 - Start 146: moldraw2DTestCatch - -146: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -146: Test timeout computed to be: 1500 145: file test2_3.png gave hash 2294574389U not the expected 2179746375U 145: Done 145: ----------------- Test 4 145: file test4_1.png gave hash 1974149556U not the expected 1403972924U 145: Done 145: ----------------- Test 5 -129: [03:17:39] diphenylmethylidencyclobutane 79.6139 -129: [03:17:39] done -129: [03:17:39] ------------------------------------- -129: [03:17:39] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -129: [03:17:39] done -129: [03:17:39] ------------------------------------- -129: [03:17:39] Test square planar complexes -129: [03:17:39] done -129: [03:17:39] ------------------------------------- -129: [03:17:39] Test octahedral complexes -129: [03:17:39] done -135/222 Test #129: testUFFForceFieldHelpers ............... Passed 3.85 sec -test 147 - Start 147: moldraw2DRxnTest1 +134/222 Test #140: pyChemicalFeatures ..................... Passed 1.99 sec +test 146 + Start 146: moldraw2DTestCatch -147: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 -147: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D -147: Test timeout computed to be: 1500 +146: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +146: Test timeout computed to be: 1500 145: file test5_1.png gave hash 2006087519U not the expected 1269428339U 145: file test5_2.png gave hash 3967299996U not the expected 3073694291U 145: file test5_3.png gave hash 2767610192U not the expected 1865192682U @@ -19942,7 +19958,6 @@ 145: ----------------- Test 6 (atom labels) 145: Done 145: ----------------- Test 7 (backgrounds) -147: ----------------- Test 1 145: file test7_1.png gave hash 4080154814U not the expected 3033050306U 145: file test7_2.png gave hash 366251741U not the expected 3476380724U 145: Done @@ -19950,35 +19965,41 @@ 145: Done 145: ----------------- Test multi-threaded drawing 145: reading molecules +135/222 Test #144: pyMolCatalog ........................... Passed 0.70 sec +test 147 + Start 147: moldraw2DRxnTest1 + +147: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 +147: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D +147: Test timeout computed to be: 1500 145: generating reference drawings +147: ----------------- Test 1 +134: [12:25:15] Molecule does not have explicit Hs. Consider calling AddHs() 147: file rxn_test1_1.png gave hash 3931149906U not the expected 1556334749U -146: Randomness seeded to: 1005124548 +146: Randomness seeded to: 2240255423 146: file contourMol_1.svg gave hash 4125787245U not the expected 2604538953U 146: file contourMol_2.svg gave hash 2850811663U not the expected 572669511U -147: file rxn_test1_2.png gave hash 665316462U not the expected 1924084263U 146: file contourMol_3.svg gave hash 1894450507U not the expected 936771429U -146: file contourMol_4.svg gave hash 4223940354U not the expected 3302971362U -146: file contourMol_5.svg gave hash 1093404576U not the expected 2230414999U 145: processing 145: launch :0 -147: file rxn_test1_3.png gave hash 583399715U not the expected 1644921059U 145: launch :1 145: launch :2 145: launch :3 +147: file rxn_test1_2.png gave hash 665316462U not the expected 1924084263U +146: file contourMol_4.svg gave hash 4223940354U not the expected 3302971362U +147: file rxn_test1_3.png gave hash 583399715U not the expected 1644921059U +146: file contourMol_5.svg gave hash 1093404576U not the expected 2230414999U 147: file rxn_test1_4.png gave hash 3197024324U not the expected 2471435686U 147: file rxn_test1_5.png gave hash 3779444276U not the expected 1428782307U -146: file testGithub3226_1.png gave hash 1298537421U not the expected 2350054896U -146: file testGithub3226_2.png gave hash 4249073986U not the expected 606206725U 147: file rxn_test1_6.png gave hash 4083260446U not the expected 483353696U -146: file testGithub3226_3.png gave hash 1401608198U not the expected 2282880418U -146: file testPNGMetadata_1.png gave hash 2404275697U not the expected 2423299691U +134: [12:25:15] Molecule does not have explicit Hs. Consider calling AddHs() 147: file rxn_test1_7.png gave hash 3485241449U not the expected 528963379U 147: Done 147: ----------------- Test 2: some examples that caused problems in testing -146: file testPNGMetadata_2.png gave hash 2335719695U not the expected 2803353117U +146: file testGithub3226_1.png gave hash 1298537421U not the expected 2350054896U 147: file rxn_test2_1.png gave hash 4000022879U not the expected 399415052U 147: 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 -146: file testGithub3369_1.svg gave hash 1012801087U not the expected 3091976328U +146: file testGithub3226_2.png gave hash 4249073986U not the expected 606206725U 147: file rxn_test2_2_1.png gave hash 1840548677U not the expected 1215378243U 147: 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 147: file rxn_test2_2_2.png gave hash 751090601U not the expected 3645141778U @@ -19986,72 +20007,62 @@ 147: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 147: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C 147: file rxn_test2_2_3.png gave hash 4146401115U not the expected 551946805U +146: file testGithub3226_3.png gave hash 1401608198U not the expected 2282880418U 147: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC -146: [03:17:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test2_2_4.png gave hash 3607216253U not the expected 4234617566U -146: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U -146: [03:17:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testPNGMetadata_1.png gave hash 2404275697U not the expected 2423299691U 147: Done 147: ----------------- Test 3: test reactant highlighting 147: file rxn_test3_1.png gave hash 663098801U not the expected 4176857511U -146: file testHandDrawn-1.png gave hash 3017698331U not the expected 698316547U 147: file rxn_test3_1.svg gave hash 2319756417U not the expected 2165658826U 147: Done 147: ----------------- Test 4: some examples from SMARTS in testing 147: draw! 147: file rxn_test4_1.png gave hash 2172852570U not the expected 4187207676U -146: [03:17:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testPNGMetadata_2.png gave hash 2335719695U not the expected 2803353117U 147: file rxn_test4_1.svg gave hash 2304233907U not the expected 3239755313U 147: done -146: file testHandDrawn-2.svg gave hash 1182231268U not the expected 4132716144U -146: [03:17:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-2.png gave hash 1476321984U not the expected 1605553248U -146: [03:17:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-3.svg gave hash 633044862U not the expected 4199337510U -146: [03:17:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-3.png gave hash 3459141761U not the expected 2881952238U -146: [03:17:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +134: [12:25:15] Molecule does not have explicit Hs. Consider calling AddHs() +146: file testGithub3369_1.svg gave hash 1012801087U not the expected 3091976328U 147: file rxn_test4_2.png gave hash 3573150360U not the expected 3490081297U -146: file testHandDrawn-4.svg gave hash 2180320567U not the expected 4197407865U -146: [03:17:39] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:39] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test4_2.svg gave hash 4061413684U not the expected 4127054729U 147: Done -146: file testHandDrawn-4.png gave hash 751103982U not the expected 3431655453U -136/222 Test #147: moldraw2DRxnTest1 ...................... Passed 0.48 sec +136/222 Test #147: moldraw2DRxnTest1 ...................... Passed 0.85 sec test 148 Start 148: pyMolDraw2D 148: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 148: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolDraw2D/Wrap 148: Test timeout computed to be: 1500 -137: 576445978 -137: =============================================================================== -137: All tests passed (73 assertions in 3 test cases) -137: -137/222 Test #137: molAlignCatchTest ...................... Passed 2.81 sec -test 149 - Start 149: testFMCS - -149: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS -149: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS -149: Test timeout computed to be: 1500 -134: .[03:17:39] Molecule does not have explicit Hs. Consider calling AddHs() -25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -148: ...[03:17:40] Font file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. -148: [03:17:40] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -25: All 191 tests passed -25: done -25: ------------------------------------- -25: Unit tests for all MMFF constraint terms. -148: ..........[03:17:40] +146: [12:25:15] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:15] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-1.svg gave hash 1143910631U not the expected 2253418236U +146: [12:25:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-1.png gave hash 3017698331U not the expected 698316547U +146: [12:25:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-2.svg gave hash 1182231268U not the expected 4132716144U +146: [12:25:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +134: [12:25:16] Molecule does not have explicit Hs. Consider calling AddHs() +146: file testHandDrawn-2.png gave hash 1476321984U not the expected 1605553248U +146: [12:25:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-3.svg gave hash 633044862U not the expected 4199337510U +146: [12:25:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-3.png gave hash 3459141761U not the expected 2881952238U +146: [12:25:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-4.svg gave hash 2180320567U not the expected 4197407865U +146: [12:25:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-4.png gave hash 751103982U not the expected 3431655453U +134: [12:25:16] Molecule does not have explicit Hs. Consider calling AddHs() +148: ...[12:25:16] Font file /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Amadeus.ttf not found. +148: [12:25:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +148: ..........[12:25:16] 148: 148: **** 148: Pre-condition Violation @@ -20060,16 +20071,43 @@ 148: Failed Expression: m 148: **** 148: -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. +148: ..................... +148: ---------------------------------------------------------------------- +148: Ran 34 tests in 0.428s +148: +148: OK +148: json lasso +134: [12:25:17] Molecule does not have explicit Hs. Consider calling AddHs() +137/222 Test #148: pyMolDraw2D ............................ Passed 1.37 sec +test 149 + Start 149: testFMCS + +149: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/testFMCS +149: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS +149: Test timeout computed to be: 1500 +132: validating reference data +83: 0,0 0 +83: 0,1 0 +83: 1,0 0 +83: 1,1 0 +83: 2,0 0 +83: 2,1 0 +138/222 Test #83: testEnumeration ........................ Passed 20.78 sec +test 150 + Start 150: pyFMCS + +150: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" +150: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap +150: Test timeout computed to be: 1500 +134: .[12:25:18] Molecule does not have explicit Hs. Consider calling AddHs() +146: file testHandDrawn-5a.svg gave hash 2478133241U not the expected 3628607349U +146: [12:25:19] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:19] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-5b.svg gave hash 2108082312U not the expected 2522138089U +146: [12:25:19] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [12:25:19] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-5.png gave hash 205144647U not the expected 3439548169U +146: file testBrackets-5a.svg gave hash 4023768529U not the expected 3061667963U 136: *********************************************************** 136: Testing O3AAlign 136: --------------------------------- @@ -20099,31 +20137,266 @@ 136: --------------------------------- 136: testMMFFO3A multithreading 136: +146: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 136: generating reference data -148: ..................... -148: ---------------------------------------------------------------------- -148: Ran 34 tests in 0.232s -148: -148: OK -148: json lasso -138/222 Test #148: pyMolDraw2D ............................ Passed 0.80 sec -test 150 - Start 150: pyFMCS - -150: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" -150: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Wrap -150: Test timeout computed to be: 1500 -25: done -139/222 Test #25: testMMFFForceField ..................... Passed 11.55 sec +146: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U +146: file testPositionVariation-1b.svg gave hash 823876785U not the expected 174339626U +146: [12:25:20] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U +146: file testGithub4238_1.png gave hash 697827931U not the expected 3410617836U +146: file testGithub4323_1.png gave hash 1827938735U not the expected 3723958844U +136: processing +136: launch :0 +136: launch :1 +136: launch :2 +136: launch :3 +146: file testGithub4323_3.png gave hash 119218767U not the expected 2185913679U +146: [12:25:20] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +149: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +149: Time elapsed 0.000 seconds +149: +149: test32() +149: 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 +149: Time elapsed 0.145 seconds +149: +149: test190() +149: 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 +149: Time elapsed 0.025 seconds +149: +149: test3() +149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds +149: Time elapsed 0.052 seconds +149: +149: testSimpleFast() +149: 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 +149: Time elapsed 0.399 seconds +149: +149: testSimple() +149: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +149: Time elapsed 0.385 seconds +149: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +149: Time elapsed 0.465 seconds +149: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds +149: Time elapsed 0.485 seconds +149: +149: testSegFault() +149: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +149: Time elapsed 0.029 seconds +149: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds +149: Time elapsed 0.031 seconds +149: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds +149: Time elapsed 0.007 seconds +149: +149: testThreshold() +149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +149: Time elapsed 0.016 seconds +149: +149: testRing1() +149: 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 +149: Time elapsed 0.886 seconds +149: 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 +149: Time elapsed 0.566 seconds +149: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds +149: Time elapsed 0.466 seconds +149: +149: testAtomCompareIsotopes() +149: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds +149: Time elapsed 0.000 seconds +149: +149: testAtomCompareAnyAtom() +149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +149: Time elapsed 0.000 seconds +149: +149: testAtomCompareAnyAtom() +149: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds +149: Time elapsed 0.000 seconds +149: +149: testAtomCompareAnyAtom() +149: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds +149: Time elapsed 0.000 seconds +149: +149: testAtomCompareAnyAtom() +149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds +149: Time elapsed 0.000 seconds +149: +149: testJnk1LigandsDistance() +149: 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 +149: Time elapsed 0.017 seconds +149: 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 +149: Time elapsed 0.001 seconds +149: +149: test18() +149: 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 +149: 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 +149: Time elapsed 0.012 seconds +149: +149: test504() +149: 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 +149: 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 +149: Time elapsed 0.212 seconds +149: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds +149: Time elapsed 0.013 seconds +149: 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 +149: Time elapsed 0.062 seconds +149: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds +149: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0172 seconds. bond[0]=6 +149: STATISTICS: +149: Total Growing Steps = 1, MCS found on 1 step, for 0.0172 seconds +149: Initial Seeds = 1, Mismatched 0 +149: Inspected Seeds = 2 +149: Rejected by BestSize = 0 +149: IndividualBondExcluded = 0 +149: MatchCheck Seeds = 2 +149: MatchCalls = 2 +149: MatchFound = 1 +149: fastMatchCalls = 1 +149: fastMatchFound = 0 +149: slowMatchCalls = 2 +149: slowMatchFound = 1 +149: DupCacheFound = 0 0 matched, 0 mismatched +149: HashCache size = 1 keys +149: HashCache size = 1 entries +149: FindHashInCache = 2 +149: HashFoundInCache= 0 +149: ExactMatchCalls = 0 +149: ExactMatchFound = 0 +149: Time elapsed 0.017 seconds +149: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 +149: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 +149: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 +149: res sub = 1 size=3 +149: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +149: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 +149: res sub = 1 size=3 +149: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds +149: test target = CC[C@H](F)Cl query = CCC useChirality = 0 +149: res sub = 1 size=3 +149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +149: test target = CC[C@H](F)Cl query = CCC useChirality = 1 +149: res sub = 1 size=3 +149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +149: test target = CCC(F)Cl query = CC useChirality = 0 +149: res sub = 1 size=2 +149: MCS: [#6]-[#6] 2 atoms, 1 bonds +149: test target = CCC(F)Cl query = CC useChirality = 1 +149: res sub = 1 size=2 +149: MCS: [#6]-[#6] 2 atoms, 1 bonds +149: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 +149: res sub = 1 size=4 +149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 +149: res sub = 1 size=4 +149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 +149: res sub = 1 size=4 +149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 +149: res sub = 1 size=4 +149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 +149: res sub = 0 size=0 +149: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +149: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 +149: res sub = 0 size=0 +149: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds +149: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 +149: res sub = 0 size=0 +149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +149: test target = OC(F)CCl query = OC(F)C useChirality = 0 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = OC(F)CCl query = OC(F)C useChirality = 1 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 +149: res sub = 0 size=0 +149: MCS: [#9] 1 atoms, 0 bonds +149: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 +149: res sub = 1 size=4 +149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds +149: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 +149: res sub = 0 size=0 +149: MCS: [#9] 1 atoms, 0 bonds +149: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 +149: res sub = 1 size=3 +149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +149: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 +149: res sub = 1 size=3 +149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +149: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 +149: res sub = 1 size=3 +149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +149: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 +149: res sub = 1 size=3 +149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds +149: +149: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> +149: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 +149: res sub = 1 size=3 +149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +149: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 +149: res sub = 1 size=3 +149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds +149: done +146: file testFlexiCanvas.2a.png gave hash 4234574492U not the expected 3217758043U +146: file testFlexiCanvas.2b.png gave hash 615048826U not the expected 4070063910U +146: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U +146: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +146: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U +146: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U +146: file testGithub4764.sz1.png gave hash 4114540222U not the expected 98827714U +146: file testGithub4764.sz2.png gave hash 868193289U not the expected 89252465U +146: file testGithub4764.sz3.png gave hash 2835449234U not the expected 148503574U +146: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U +146: file github5383_1.svg gave hash 2850811663U not the expected 3666750661U +146: file github5383_2.svg gave hash 1346330069U not the expected 0U +146: file github5383_1.png gave hash 3310569434U not the expected 992803933U +146: file acs1996_1.png gave hash 1909632721U not the expected 2957839025U +146: file acs1996_2.png gave hash 1539606209U not the expected 2664798808U +146: file acs1996_3.svg gave hash 510450189U not the expected 879041204U +146: file acs1996_8.svg gave hash 10362698U not the expected 2477908768U +146: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U +146: [12:25:22] 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. +146: file bond_highlights_8.svg gave hash 1272407071U not the expected 2956924065U +146: file test_github5947.svg gave hash 4282730978U not the expected 337972125U +132: processing +132: launch :0 +132: launch :1 +132: launch :2 +132: launch :3 +146: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U +146: file github6336_1.png gave hash 1930712448U not the expected 2958833204U +146: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U +146: file github6504_2.svg gave hash 106020287U not the expected 2871662880U +146: file github6569_1.svg gave hash 1698514747U not the expected 116573839U +146: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U +146: =============================================================================== +146: All tests passed (6525 assertions in 94 test cases) +146: +139/222 Test #146: moldraw2DTestCatch ..................... Passed 7.94 sec test 151 Start 151: FMCStest 151: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 151: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/FMCS/Test 151: Test timeout computed to be: 1500 -146: file testHandDrawn-5a.svg gave hash 2478133241U not the expected 3628607349U -146: [03:17:40] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:40] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory 151: fopen testChEMBL_Txt(): No such file or directory @@ -22089,49 +22362,30 @@ 151: 151: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 151: ERROR: RDKit could not load input file -146: file testHandDrawn-5b.svg gave hash 2108082312U not the expected 2522138089U -146: [03:17:40] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [03:17:40] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -140/222 Test #151: FMCStest ............................... Passed 0.04 sec +140/222 Test #151: FMCStest ............................... Passed 0.11 sec test 152 Start 152: molHashCatchTest 152: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 152: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash 152: Test timeout computed to be: 1500 -146: file testHandDrawn-5.png gave hash 205144647U not the expected 3439548169U -146: file testBrackets-5a.svg gave hash 4023768529U not the expected 3061667963U -146: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -146: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -146: file testPositionVariation-1b.svg gave hash 823876785U not the expected 174339626U -152: Randomness seeded to: 2703433503 +152: Randomness seeded to: 2560559548 152: =============================================================================== 152: All tests passed (304 assertions in 9 test cases) 152: -141/222 Test #152: molHashCatchTest ....................... Passed 0.07 sec +141/222 Test #152: molHashCatchTest ....................... Passed 0.09 sec test 153 Start 153: pyMolHash 153: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 153: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolHash/Wrap 153: Test timeout computed to be: 1500 -132: validating reference data -146: [03:17:40] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U -146: file testGithub4238_1.png gave hash 697827931U not the expected 3410617836U -146: file testGithub4323_1.png gave hash 1827938735U not the expected 3723958844U -136: processing -136: launch :0 -136: launch :1 -136: launch :2 -136: launch :3 -146: file testGithub4323_3.png gave hash 119218767U not the expected 2185913679U -146: [03:17:40] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 153: ... 153: ---------------------------------------------------------------------- -153: Ran 3 tests in 0.015s +153: Ran 3 tests in 0.031s 153: 153: OK -142/222 Test #153: pyMolHash .............................. Passed 0.39 sec +142/222 Test #153: pyMolHash .............................. Passed 1.05 sec test 154 Start 154: testMMPA @@ -22140,7 +22394,7 @@ 154: Test timeout computed to be: 1500 154: 154: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -154: Time elapsed 0.001815 seconds +154: Time elapsed 0.017990 seconds 154: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -22181,7 +22435,7 @@ 154: --- UNMATCHED Reference RESULTS: --- 154: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 154: ----------------------------------- -154: Time elapsed 0.001726 seconds +154: Time elapsed 0.009783 seconds 154: 154: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 154: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -22223,7 +22477,7 @@ 154: ----------------------------------- 154: 154: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -154: Time elapsed 0.001604 seconds +154: Time elapsed 0.001649 seconds 154: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 154: 1: PASSED. matchedRefRes = 4 154: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] @@ -22263,7 +22517,7 @@ 154: ----------------------------------- 154: 154: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -154: Time elapsed 0.000464 seconds +154: Time elapsed 0.000447 seconds 154: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 154: 1: PASSED. matchedRefRes = 2 154: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -22285,7 +22539,7 @@ 154: ----------------------------------- 154: 154: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -154: Time elapsed 0.001647 seconds +154: Time elapsed 0.017862 seconds 154: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -22328,7 +22582,7 @@ 154: ----------------------------------- 154: 154: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -154: Time elapsed 0.001778 seconds +154: Time elapsed 0.013991 seconds 154: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -22369,297 +22623,38 @@ 154: --- ALL PASSED --- 154: ----------------------------------- 154: 5 TEST CASES FAILED -143/222 Test #154: testMMPA ............................... Passed 0.12 sec +143/222 Test #154: testMMPA ............................... Passed 0.26 sec test 155 Start 155: pyMMPA 155: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" 155: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MMPA/Wrap 155: Test timeout computed to be: 1500 -146: file testFlexiCanvas.2a.png gave hash 4234574492U not the expected 3217758043U -146: file testFlexiCanvas.2b.png gave hash 615048826U not the expected 4070063910U -146: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U -146: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -146: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -146: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U -146: file testGithub4764.sz1.png gave hash 4114540222U not the expected 98827714U -146: file testGithub4764.sz2.png gave hash 868193289U not the expected 89252465U -146: file testGithub4764.sz3.png gave hash 2835449234U not the expected 148503574U -146: file testGithub_5061.svg gave hash 4026821599U not the expected 83338095U -146: file github5383_1.svg gave hash 2850811663U not the expected 3666750661U -146: file github5383_2.svg gave hash 1346330069U not the expected 0U -146: file github5383_1.png gave hash 3310569434U not the expected 992803933U -146: file acs1996_1.png gave hash 1909632721U not the expected 2957839025U -146: file acs1996_2.png gave hash 1539606209U not the expected 2664798808U -146: file acs1996_3.svg gave hash 510450189U not the expected 879041204U -146: file acs1996_8.svg gave hash 10362698U not the expected 2477908768U -146: file acs1996_10.svg gave hash 1008047306U not the expected 2229333301U -146: [03:17:41] 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. -146: file bond_highlights_8.svg gave hash 1272407071U not the expected 2956924065U -146: file test_github5947.svg gave hash 4282730978U not the expected 337972125U -146: file test_github6112.svg gave hash 3291975047U not the expected 3278777629U -146: file github6336_1.png gave hash 1930712448U not the expected 2958833204U -146: file github6504_1.svg gave hash 3649936662U not the expected 1429448598U -146: file github6504_2.svg gave hash 106020287U not the expected 2871662880U -146: file github6569_1.svg gave hash 1698514747U not the expected 116573839U -146: file github6569_2.svg gave hash 2778768241U not the expected 2367779037U -146: =============================================================================== -146: All tests passed (6525 assertions in 94 test cases) -146: -144/222 Test #146: moldraw2DTestCatch ..................... Passed 2.36 sec +149: [12:25:25] The provided InitialSeed is not an MCS and will be ignored +25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: done +25: ------------------------------------- +25: Unit tests for all MMFF constraint terms. +25: 10.0003 +25: done +25: ------------------------------------- +25: Unit test for MMFF TorsionConstraint close to 0 degrees. +25: done +25: ------------------------------------- +25: Unit tests for copying MMFF ForceFields. +25: done +25: ------------------------------------- +25: Unit test for MMFF butane scan. +25: done +144/222 Test #25: testMMFFForceField ..................... Passed 34.31 sec test 156 Start 156: testRascalMCES 156: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES 156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES 156: Test timeout computed to be: 1500 -149: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -149: Time elapsed 0.000 seconds -149: -149: test32() -149: 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 -149: Time elapsed 0.069 seconds -149: -149: test190() -149: 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 -149: Time elapsed 0.009 seconds -149: -149: test3() -149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -149: Time elapsed 0.016 seconds -149: -149: testSimpleFast() -149: 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 -149: Time elapsed 0.109 seconds -149: -149: testSimple() -149: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -149: Time elapsed 0.111 seconds -149: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -149: Time elapsed 0.120 seconds -149: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -149: Time elapsed 0.117 seconds -149: -149: testSegFault() -149: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -149: Time elapsed 0.013 seconds -149: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -149: Time elapsed 0.015 seconds -149: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds -149: Time elapsed 0.015 seconds -149: -149: testThreshold() -149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -149: Time elapsed 0.000 seconds -149: -149: testRing1() -149: 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 -149: Time elapsed 0.360 seconds -149: 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 -149: Time elapsed 0.358 seconds -149: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds -149: Time elapsed 0.398 seconds -149: -149: testAtomCompareIsotopes() -149: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -149: Time elapsed 0.000 seconds -149: -149: testAtomCompareAnyAtom() -149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -149: Time elapsed 0.000 seconds -149: -149: testAtomCompareAnyAtom() -149: MCS: [#6]1-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6]-,:1=,-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds -149: Time elapsed 0.000 seconds -149: -149: testAtomCompareAnyAtom() -149: MCS: [#1]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 8 atoms, 8 bonds -149: Time elapsed 0.008 seconds -149: -149: testAtomCompareAnyAtom() -149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#8] 7 atoms, 7 bonds -149: Time elapsed 0.000 seconds -149: -149: testJnk1LigandsDistance() -149: 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 -149: Time elapsed 0.013 seconds -149: 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 -149: Time elapsed 0.001 seconds -149: -149: test18() -149: 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 -149: 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 -149: Time elapsed 0.012 seconds -149: -149: test504() -149: 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 -149: 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 -149: Time elapsed 0.099 seconds -149: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -149: Time elapsed 0.001 seconds -149: 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 -149: Time elapsed 0.031 seconds -149: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -149: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0009 seconds. bond[0]=6 -149: STATISTICS: -149: Total Growing Steps = 1, MCS found on 1 step, for 0.0009 seconds -149: Initial Seeds = 1, Mismatched 0 -149: Inspected Seeds = 2 -149: Rejected by BestSize = 0 -149: IndividualBondExcluded = 0 -149: MatchCheck Seeds = 2 -149: MatchCalls = 2 -149: MatchFound = 1 -149: fastMatchCalls = 1 -149: fastMatchFound = 0 -149: slowMatchCalls = 2 -149: slowMatchFound = 1 -149: DupCacheFound = 0 0 matched, 0 mismatched -149: HashCache size = 1 keys -149: HashCache size = 1 entries -149: FindHashInCache = 2 -149: HashFoundInCache= 0 -149: ExactMatchCalls = 0 -149: ExactMatchFound = 0 -149: Time elapsed 0.001 seconds -149: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 -149: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 -149: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 -149: res sub = 1 size=3 -149: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -149: test target = O[C@H](F)CCl query = C(F)C useChirality = 1 -149: res sub = 1 size=3 -149: MCS: [#6](-[#9])-[#6] 3 atoms, 2 bonds -149: test target = CC[C@H](F)Cl query = CCC useChirality = 0 -149: res sub = 1 size=3 -149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -149: test target = CC[C@H](F)Cl query = CCC useChirality = 1 -149: res sub = 1 size=3 -149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -149: test target = CCC(F)Cl query = CC useChirality = 0 -149: res sub = 1 size=2 -149: MCS: [#6]-[#6] 2 atoms, 1 bonds -149: test target = CCC(F)Cl query = CC useChirality = 1 -149: res sub = 1 size=2 -149: MCS: [#6]-[#6] 2 atoms, 1 bonds -149: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 0 -149: res sub = 1 size=4 -149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = C[C@H](F)CCl query = C[C@H](F)C useChirality = 1 -149: res sub = 1 size=4 -149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 0 -149: res sub = 1 size=4 -149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = C[C@H](F)CCl query = C[C@@H](F)C useChirality = 1 -149: res sub = 1 size=4 -149: MCS: [#6]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = O[C@H](F)CCl query = CC(F)C useChirality = 0 -149: res sub = 0 size=0 -149: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -149: test target = O[C@H](F)CCl query = CC(F)C useChirality = 1 -149: res sub = 0 size=0 -149: MCS: [#6]-[#6]-[#9] 3 atoms, 2 bonds -149: test target = O[C@H](F)CCl query = OC(F)C useChirality = 0 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = O[C@H](F)CCl query = OC(F)C useChirality = 1 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 0 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = O[C@H](F)CCl query = O[C@H](F)C useChirality = 1 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 0 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = O[C@H](F)CCl query = O[C@@H](F)C useChirality = 1 -149: res sub = 0 size=0 -149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -149: test target = OC(F)CCl query = OC(F)C useChirality = 0 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = OC(F)CCl query = OC(F)C useChirality = 1 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = OC(F)CCl query = O[C@H](F)C useChirality = 0 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = OC(F)CCl query = O[C@H](F)C useChirality = 1 -149: res sub = 0 size=0 -149: MCS: [#9] 1 atoms, 0 bonds -149: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 0 -149: res sub = 1 size=4 -149: MCS: [#8]-[#6](-[#9])-[#6] 4 atoms, 3 bonds -149: test target = OC(F)CCl query = O[C@@H](F)C useChirality = 1 -149: res sub = 0 size=0 -149: MCS: [#9] 1 atoms, 0 bonds -149: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 0 -149: res sub = 1 size=3 -149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -149: test target = O[C@H](F)CCl query = O[C@H]C useChirality = 1 -149: res sub = 1 size=3 -149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -149: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 0 -149: res sub = 1 size=3 -149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -149: test target = O[C@H](F)CCl query = O[C@@H]C useChirality = 1 -149: res sub = 1 size=3 -149: MCS: [#8]-[#6]-[#6] 3 atoms, 2 bonds -149: -149: 0. <<<<<<<<< actual MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds >>>>>>> -149: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 0 -149: res sub = 1 size=3 -149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -149: test target = CC[C@H](F)Cl query = CC[C@H] useChirality = 1 -149: res sub = 1 size=3 -149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds -149: done -132: processing -132: launch :0 -132: launch :1 -132: launch :2 -132: launch :3 -155: ......... -155: ---------------------------------------------------------------------- -155: Ran 9 tests in 1.444s -155: -155: OK -145/222 Test #155: pyMMPA ................................. Passed 1.94 sec -test 157 - Start 157: testRascalCluster - -157: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster -157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES -157: Test timeout computed to be: 1500 -149: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: ........................................[03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: .[03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: .[03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: .[03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: [03:17:43] The provided InitialSeed is not an MCS and will be ignored -150: ................. -150: ---------------------------------------------------------------------- -150: Ran 60 tests in 3.309s -150: -150: OK -146/222 Test #150: pyFMCS ................................. Passed 3.73 sec -test 158 - Start 158: pyMolDraw2D - -158: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" -158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap -158: Test timeout computed to be: 1500 -134: ..[03:17:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +134: ..[12:25:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 145: Done 145: ----------------- Test Github #781: Rendering single-atom molecules 145: Done @@ -22677,27 +22672,51 @@ 145: Done 145: ----------------- Test Github774: upside-down drawings 145: file test774_1.png gave hash 3121030024U not the expected 927423591U +155: ......... +155: ---------------------------------------------------------------------- +155: Ran 9 tests in 3.884s +155: +155: OK 145: file test774_2.png gave hash 2368659339U not the expected 1171827286U 145: Done 145: ----------------- Test 9 (molecule legends) 145: file test9_1.svg gave hash 923579170U not the expected 1484349178U 145: Done 145: ----------------- Test Github852: Lines used to wedge bonds are too thick +150: ........................................[12:25:29] The provided InitialSeed is not an MCS and will be ignored +150: [12:25:29] The provided InitialSeed is not an MCS and will be ignored +150: [12:25:29] The provided InitialSeed is not an MCS and will be ignored 145: file test852_1.png gave hash 2345477955U not the expected 736085072U +150: .[12:25:29] The provided InitialSeed is not an MCS and will be ignored 145: file test852_2.png gave hash 2980031162U not the expected 1438089260U 145: ---------------- +150: [12:25:29] The provided InitialSeed is not an MCS and will be ignored 145: ---------------- 145: ---------------- 145: ---------------- 145: Done 145: ----------------- Test Github860: Atom symbols in wrong order if bond comes from right +150: [12:25:29] The provided InitialSeed is not an MCS and will be ignored 145: file test860_1.png gave hash 988661147U not the expected 2065140854U +150: .[12:25:29] The provided InitialSeed is not an MCS and will be ignored +150: [12:25:29] The provided InitialSeed is not an MCS and will be ignored +150: [12:25:29] The provided InitialSeed is not an MCS and will be ignored 145: file test860_2.png gave hash 1783539966U not the expected 3098360765U +150: .[12:25:29] The provided InitialSeed is not an MCS and will be ignored +150: [12:25:29] The provided InitialSeed is not an MCS and will be ignored 145: file test860_3.png gave hash 55970806U not the expected 3439618110U 145: Done 145: ----------------- Test Github #910: ugly coordinates generated for peptide chains +150: [12:25:29] The provided InitialSeed is not an MCS and will be ignored 145: Done 145: ----------------- Test Github #932: mistake in SVG for wedged bonds +145/222 Test #155: pyMMPA ................................. Passed 5.14 sec +test 157 + Start 157: testRascalCluster + +157: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster +157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES +157: Test timeout computed to be: 1500 145: Done 145: ----------------- Test Github #953: default color should not be cyan 145: Done @@ -22712,6 +22731,11 @@ 145: file test10_6.svg gave hash 2996130233U not the expected 961103536U 145: Done 145: ----------------- Testing drawing a grid of molecules +150: ................. +150: ---------------------------------------------------------------------- +150: Ran 60 tests in 10.919s +150: +150: OK 145: Done 145: ----------------- Testing drawMolecules 145: file test12_1.svg gave hash 2982175789U not the expected 881731720U @@ -22735,6 +22759,13 @@ 145: ----------------- Testing github 1829: crash when drawMolecules() is called with an empty list 145: Done 145: ----------------- Testing use of fixed scales for drawing. +146/222 Test #150: pyFMCS ................................. Passed 11.99 sec +test 158 + Start 158: pyMolDraw2D + +158: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" +158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RascalMCES/Wrap +158: Test timeout computed to be: 1500 145: Done 145: ----------------- Testing rotation of 2D drawing. 145: Done @@ -22785,59 +22816,59 @@ 145: Done 145: ----------------- Test AND queries 145: Done -147/222 Test #145: moldraw2DTest1 ......................... Passed 6.83 sec +147/222 Test #145: moldraw2DTest1 ......................... Passed 16.10 sec test 159 Start 159: testCIPLabeler 159: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 159: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler 159: Test timeout computed to be: 1500 -159: Randomness seeded to: 1810350150 -159: [03:17:45] non kekulizable aromatic bond being treated as bond order 1 -159: [03:17:45] non kekulizable aromatic bond being treated as bond order 1 -159: [03:17:45] non kekulizable aromatic bond being treated as bond order 1 -159: [03:17:45] non kekulizable aromatic bond being treated as bond order 1 -159: [03:17:45] non kekulizable aromatic bond being treated as bond order 1 -159: [03:17:45] non kekulizable aromatic bond being treated as bond order 1 +159: Randomness seeded to: 2239518435 +159: [12:25:30] non kekulizable aromatic bond being treated as bond order 1 +159: [12:25:30] non kekulizable aromatic bond being treated as bond order 1 +159: [12:25:30] non kekulizable aromatic bond being treated as bond order 1 +159: [12:25:30] non kekulizable aromatic bond being treated as bond order 1 +159: [12:25:30] non kekulizable aromatic bond being treated as bond order 1 +159: [12:25:30] non kekulizable aromatic bond being treated as bond order 1 159: =============================================================================== 159: All tests passed (5977 assertions in 13 test cases) 159: -148/222 Test #159: testCIPLabeler ......................... Passed 0.13 sec +148/222 Test #159: testCIPLabeler ......................... Passed 0.46 sec test 160 Start 160: pyCIPLabelsWrapTest 160: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 160: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 160: Test timeout computed to be: 1500 -158: ........ -158: ---------------------------------------------------------------------- -158: Ran 8 tests in 1.271s -158: -158: OK -149/222 Test #158: pyMolDraw2D ............................ Passed 2.24 sec +160: ... +160: ---------------------------------------------------------------------- +160: Ran 3 tests in 0.022s +160: +160: OK +149/222 Test #160: pyCIPLabelsWrapTest .................... Passed 1.56 sec test 161 Start 161: pyCIPLabelsValidation 161: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 161: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 161: Test timeout computed to be: 1500 -160: ... -160: ---------------------------------------------------------------------- -160: Ran 3 tests in 0.014s -160: -160: OK -150/222 Test #160: pyCIPLabelsWrapTest .................... Passed 0.61 sec +158: ........ +158: ---------------------------------------------------------------------- +158: Ran 8 tests in 3.195s +158: +158: OK +150/222 Test #158: pyMolDraw2D ............................ Passed 4.45 sec test 162 Start 162: deprotectTest 162: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect/deprotectTest 162: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Deprotect 162: Test timeout computed to be: 1500 -162: Randomness seeded to: 3779977479 +162: Randomness seeded to: 3110153582 162: =============================================================================== 162: All tests passed (111 assertions in 3 test cases) 162: -151/222 Test #162: deprotectTest .......................... Passed 0.05 sec +151/222 Test #162: deprotectTest .......................... Passed 0.25 sec test 163 Start 163: pyDeprotect @@ -22846,7 +22877,7 @@ 163: Test timeout computed to be: 1500 163: ..... 163: ---------------------------------------------------------------------- -163: Ran 5 tests in 0.023s +163: Ran 5 tests in 0.090s 163: 163: OK 163: Testing tert-butyldimethylsilyl @@ -22899,7 +22930,7 @@ 163: Testing acetamide 163: Testing carbobenzyloxy 163: Testing Acetal/Ketal -152/222 Test #163: pyDeprotect ............................ Passed 0.32 sec +152/222 Test #163: pyDeprotect ............................ Passed 1.42 sec test 164 Start 164: testReducedGraphs @@ -22924,7 +22955,7 @@ 164: 164: 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, ] 164: -153/222 Test #164: testReducedGraphs ...................... Passed 0.03 sec +153/222 Test #164: testReducedGraphs ...................... Passed 0.09 sec test 165 Start 165: pyReducedGraphs @@ -22933,82 +22964,492 @@ 165: Test timeout computed to be: 1500 165: ..... 165: ---------------------------------------------------------------------- -165: Ran 5 tests in 0.010s +165: Ran 5 tests in 0.037s 165: 165: OK -154/222 Test #165: pyReducedGraphs ........................ Passed 0.28 sec +154/222 Test #165: pyReducedGraphs ........................ Passed 1.09 sec test 166 Start 166: trajectoryTest 166: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest 166: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Trajectory 166: Test timeout computed to be: 1500 -155/222 Test #166: trajectoryTest ......................... Passed 0.17 sec +155/222 Test #166: trajectoryTest ......................... Passed 0.76 sec test 167 Start 167: substructLibraryTest 167: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest 167: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 167: Test timeout computed to be: 1500 -167: [03:17:47] ------------------------------------- -167: [03:17:47] Test1 -167: [03:17:47] done -167: [03:17:47] ------------------------------------- -167: [03:17:47] Test2 -167: [03:17:48] done -167: [03:17:48] ------------------------------------- -167: [03:17:48] Test3 (stereo options) -167: [03:17:48] Done (stereo options) -167: [03:17:48] ------------------------------------- -167: [03:17:48] Test4 (trusted smiles) -167: [03:17:48] Done (trusted smiles) -167: [03:17:48] ------------------------------------- -167: [03:17:48] Testing C++ docs -167: [03:17:48] Done (C++ doc tests) -167: [03:17:48] ------------------------------------- -167: [03:17:48] Testing C++ ring query: PatternHolder -167: [03:17:48] Done (C++ ring query tests) -167: [03:17:48] ------------------------------------- -167: [03:17:48] Testing C++ ring query: TautomerPatternHolder -167: [03:17:48] Done (C++ ring query tests) -167: [03:17:48] ------------------------------------- -167: [03:17:48] Add Patterns -157: Randomness seeded to: 2317721215 +167: [12:25:38] ------------------------------------- +167: [12:25:38] Test1 +156: Randomness seeded to: 188869862 +156: Timed out after 11 seconds. +167: [12:25:38] done +167: [12:25:38] ------------------------------------- +167: [12:25:38] Test2 +167: [12:25:39] done +167: [12:25:39] ------------------------------------- +167: [12:25:39] Test3 (stereo options) +167: [12:25:39] Done (stereo options) +167: [12:25:39] ------------------------------------- +167: [12:25:39] Test4 (trusted smiles) +167: [12:25:39] Done (trusted smiles) +167: [12:25:39] ------------------------------------- +167: [12:25:39] Testing C++ docs +167: [12:25:39] Done (C++ doc tests) +167: [12:25:39] ------------------------------------- +167: [12:25:39] Testing C++ ring query: PatternHolder +167: [12:25:39] Done (C++ ring query tests) +167: [12:25:39] ------------------------------------- +167: [12:25:39] Testing C++ ring query: TautomerPatternHolder +167: [12:25:39] Done (C++ ring query tests) +167: [12:25:39] ------------------------------------- +167: [12:25:39] Add Patterns +138: .............[12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:40] Molecule does not have explicit Hs. Consider calling AddHs() +157: Randomness seeded to: 933784943 157: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -138: .............[03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:48] Molecule does not have explicit Hs. Consider calling AddHs() -138: ...[03:17:50] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:50] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:50] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:50] Molecule does not have explicit Hs. Consider calling AddHs() -138: [03:17:50] Molecule does not have explicit Hs. Consider calling AddHs() +138: ...[12:25:45] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:45] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:45] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:45] Molecule does not have explicit Hs. Consider calling AddHs() +138: [12:25:45] Molecule does not have explicit Hs. Consider calling AddHs() +167: [12:25:45] ------------------------------------- +167: [12:25:45] testing PatternHolder 138: ... 138: ---------------------------------------------------------------------- -138: Ran 19 tests in 12.257s +138: Ran 19 tests in 32.678s 138: 138: OK 138: Testing MolAlign Wrappers -156/222 Test #138: pyMolAlign ............................. Passed 13.10 sec +167: [12:25:46] ------------------------------------- +167: [12:25:46] testing TautomerPatternHolder +156/222 Test #138: pyMolAlign ............................. Passed 33.54 sec test 168 Start 168: substructLibraryCatchTest 168: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 168: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SubstructLibrary 168: Test timeout computed to be: 1500 -168: Randomness seeded to: 2405474672 +167: [12:25:46] ------------------------------------- +167: [12:25:46] testSegFaultInHolder +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: syntax error while parsing: [12:25:46] dsafsdfSMILES +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf[12:25:46] Parse Error: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: ' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error[12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: +167: [12:25:46] SMILES Parse Error: [12:25:46] SMILES Parse Error: syntax errorFailed parsing SMILES 'dsafsdf'SMILES Parse Error: syntax error[12:25:46] SMILES Parse Error: while parsing: syntax error[12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [12:25:46] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [12:25:46] ------------------------------------- +167: [12:25:46] Results do not depend on numThreads +168: Randomness seeded to: 2525863921 168: =============================================================================== 168: All tests passed (171 assertions in 5 test cases) 168: -157/222 Test #168: substructLibraryCatchTest .............. Passed 1.45 sec +157/222 Test #168: substructLibraryCatchTest .............. Passed 2.13 sec test 169 Start 169: pySubstructLibrary @@ -23317,17 +23758,15 @@ 161: VS300: PASSED 161: Check finished: 0 molecules failed. 161: Failed: -158/222 Test #161: pyCIPLabelsValidation .................. Passed 5.67 sec +158/222 Test #161: pyCIPLabelsValidation .................. Passed 18.25 sec test 170 Start 170: testRGroupDecomp 170: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 170: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 170: Test timeout computed to be: 1500 -170: [03:17:52] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -170: [03:17:52] WARNING: not removing hydrogen atom with dummy atom neighbors -156: Randomness seeded to: 821796644 -156: Timed out after 11 seconds. +170: [12:25:52] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +170: [12:25:52] WARNING: not removing hydrogen atom with dummy atom neighbors 136: --------------------------------- 136: test O3A multithreading bug 136: @@ -23335,653 +23774,213 @@ 136: testCrippenO3A multithreading 136: 136: generating reference data -167: [03:17:53] ------------------------------------- -167: [03:17:53] testing PatternHolder +136: processing +136: launch :0 +136: launch :1 +136: launch :2 +136: launch :3 149: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -149: TOTAL Time elapsed 13.58 seconds -159/222 Test #149: testFMCS ............................... Passed 13.63 sec +149: TOTAL Time elapsed 37.46 seconds +159/222 Test #149: testFMCS ............................... Passed 37.60 sec test 171 Start 171: testRGroupDecompInternals 171: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 171: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 171: Test timeout computed to be: 1500 -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [03:17:53] WARNING: not removing hydrogen atom with dummy atom neighbors -160/222 Test #171: testRGroupDecompInternals .............. Passed 0.03 sec +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [12:25:54] WARNING: not removing hydrogen atom with dummy atom neighbors +160/222 Test #171: testRGroupDecompInternals .............. Passed 0.15 sec test 172 Start 172: rgroupCatchTests 172: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 172: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition 172: Test timeout computed to be: 1500 -136: processing -136: launch :0 -136: launch :1 -136: launch :2 -136: launch :3 -172: Randomness seeded to: 3839232955 +172: Randomness seeded to: 1383830498 172: =============================================================================== 172: All tests passed (203 assertions in 13 test cases) 172: -161/222 Test #172: rgroupCatchTests ....................... Passed 0.14 sec +161/222 Test #172: rgroupCatchTests ....................... Passed 0.73 sec test 173 Start 173: pyRGroupDecomposition 173: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 173: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap 173: Test timeout computed to be: 1500 -167: [03:17:53] ------------------------------------- -167: [03:17:53] testing TautomerPatternHolder -167: [03:17:53] ------------------------------------- -167: [03:17:53] testSegFaultInHolder -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: [03:17:53] syntax error while parsing: dsafsdf -167: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: ' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILESSMILES Parse Error: syntax error while parsing: dsafsdf -167: Parse Error: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error[03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] [03:17:53] [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'SMILES Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: '[03:17:53] SMILES Parse Error: syntax error -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -170: iterative -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [03:17:53] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [03:17:53] ------------------------------------- -167: [03:17:53] Results do not depend on numThreads -170: bulk -134: ......[03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: .[03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: .[03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: [03:17:54] Molecule does not have explicit Hs. Consider calling AddHs() -134: . -134: ---------------------------------------------------------------------- -134: Ran 19 tests in 18.732s -134: -134: OK -162/222 Test #134: pyDistGeomHelpers ...................... Passed 19.17 sec +167: [12:25:56] ------------------------------------- +167: [12:25:56] Results do not depend on numThreads (all same) +167: [12:25:56] ------------------------------------- +167: [12:25:56] testTautomerQueries +167: [12:25:56] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +167: [12:25:56] ------------------------------------- +167: [12:25:56] github3881 recursive smarts with rings +162/222 Test #167: substructLibraryTest ................... Passed 18.69 sec test 174 Start 174: molInterchangeTest1 174: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 174: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 174: Test timeout computed to be: 1500 -173: .................. -173: ---------------------------------------------------------------------- -173: Ran 18 tests in 1.085s -173: -173: OK -174: [03:17:54] test1: basics -174: [03:17:54] done -174: [03:17:54] test2: basic writing +174: [12:25:56] test1: basics +174: [12:25:56] done +174: [12:25:56] test2: basic writing 174: {"rdkitjson":{"version":11},"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":"2023.09.3","cipRanks":[0,0]}]}]} 174: {"rdkitjson":{"version":11},"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":"2023.09.3","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 174: {"rdkitjson":{"version":11},"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":"2023.09.3","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]]}]}]} 174: {"rdkitjson":{"version":11},"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":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} -174: [03:17:54] done -174: [03:17:54] test3: writing conformers +174: [12:25:56] done +174: [12:25:56] test3: writing conformers 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1987,-0.0452],[-0.3332,0.4555],[0.1659,1.322],[0.5332,-0.0438],[-2.0652,0.4541],[-0.8339,1.3212]]},{"dim":3,"coords":[[0.9553,-0.3743,-0.4679],[-0.3616,-0.131,-0.0794],[-0.5097,1.6255,0.1705],[-0.5778,-0.7919,1.1042],[1.5276,0.1063,0.1627],[-1.0339,-0.4345,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2023.09.3","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -174: [03:17:54] done -174: [03:17:54] test4: writing properties +174: [12:25:56] done +174: [12:25:56] test4: writing properties 174: {"rdkitjson":{"version":11},"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":"2023.09.3","cipRanks":[0,0]}]}]} -174: [03:17:54] done -174: [03:17:54] test5: writing partial charges +174: [12:25:56] done +174: [12:25:56] test5: writing partial charges 174: {"rdkitjson":{"version":11},"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":"2023.09.3","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2023.09.3","values":[0.5,-0.5]}]}]} -174: [03:17:54] testing parse options -174: [03:17:54] done -174: [03:17:54] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +174: [12:25:56] testing parse options +174: [12:25:56] done +174: [12:25:56] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 174: {"rdkitjson":{"version":11},"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":"2023.09.3","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -174: [03:17:54] done -174: [03:17:54] testing 'either' stereochemistry -174: [03:17:54] done -163/222 Test #174: molInterchangeTest1 .................... Passed 0.03 sec +174: [12:25:56] done +174: [12:25:56] testing 'either' stereochemistry +174: [12:25:56] done +163/222 Test #174: molInterchangeTest1 .................... Passed 0.07 sec test 175 Start 175: molInterchangeCatchTest 175: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest 175: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange 175: Test timeout computed to be: 1500 -175: Randomness seeded to: 186857402 -175: [03:17:54] unrecognized bond type 12 set to zero while writing -175: [03:17:54] unrecognized bond type 0 set to zero while writing +175: Randomness seeded to: 2063953932 +175: [12:25:56] unrecognized bond type 12 set to zero while writing +175: [12:25:56] unrecognized bond type 0 set to zero while writing 175: =============================================================================== 175: All tests passed (117 assertions in 5 test cases) 175: -164/222 Test #173: pyRGroupDecomposition .................. Passed 1.35 sec -165/222 Test #175: molInterchangeCatchTest ................ Passed 0.05 sec +164/222 Test #175: molInterchangeCatchTest ................ Passed 0.08 sec test 176 Start 176: pyMolInterchange 176: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 176: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolInterchange/Wrap 176: Test timeout computed to be: 1500 +176: .. +176: ---------------------------------------------------------------------- +176: Ran 2 tests in 0.039s +176: +176: OK +165/222 Test #176: pyMolInterchange ....................... Passed 1.08 sec test 177 Start 177: testSLNParse 177: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/testSLNParse 177: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse 177: Test timeout computed to be: 1500 -177: [03:17:55] SLN Parse Error: syntax error while parsing: CH4[I=13] -177: [03:17:55] Failed parsing SLN 'CH4[I=13]' -177: [03:17:55] SLN Parser error: Atom ID 1 appears *after* its ring closure. -177: [03:17:55] SLN Parser error: Ring closure 1 does not have a corresponding opener. -177: [03:17:55] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -177: [03:17:55] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -177: [03:17:55] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -177: [03:17:55] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -177: [03:17:55] SLN Parse Error: syntax error while parsing: CH4 fff -177: [03:17:55] Failed parsing SLN 'CH4 fff' -177: [03:17:55] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -177: [03:17:55] Failed parsing SLN 'C[charge=+1] foo' -177: [03:17:55] Query property 'is' ignored on non-query atom -177: [03:17:55] Query property 'is' ignored on non-query atom -166/222 Test #177: testSLNParse ........................... Passed 0.05 sec +177: [12:25:57] SLN Parse Error: syntax error while parsing: CH4[I=13] +177: [12:25:57] Failed parsing SLN 'CH4[I=13]' +177: [12:25:57] SLN Parser error: Atom ID 1 appears *after* its ring closure. +177: [12:25:57] SLN Parser error: Ring closure 1 does not have a corresponding opener. +177: [12:25:57] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +177: [12:25:57] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +177: [12:25:57] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +177: [12:25:57] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +177: [12:25:57] SLN Parse Error: syntax error while parsing: CH4 fff +177: [12:25:57] Failed parsing SLN 'CH4 fff' +177: [12:25:57] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +177: [12:25:57] Failed parsing SLN 'C[charge=+1] foo' +177: [12:25:58] Query property 'is' ignored on non-query atom +177: [12:25:58] Query property 'is' ignored on non-query atom +166/222 Test #177: testSLNParse ........................... Passed 0.09 sec test 178 Start 178: pySLNParse 178: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" 178: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/SLNParse/Wrap 178: Test timeout computed to be: 1500 -176: .. -176: ---------------------------------------------------------------------- -176: Ran 2 tests in 0.020s -176: -176: OK -167/222 Test #176: pyMolInterchange ....................... Passed 0.47 sec +178: .. +178: ---------------------------------------------------------------------- +178: Ran 2 tests in 0.019s +178: +178: OK +167/222 Test #178: pySLNParse ............................. Passed 0.99 sec test 179 Start 179: pyGraphMolWrap 179: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rough_test.py" 179: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 179: Test timeout computed to be: 1500 -178: .. -178: ---------------------------------------------------------------------- -178: Ran 2 tests in 0.006s -178: -178: OK -168/222 Test #178: pySLNParse ............................. Passed 0.50 sec +170: iterative +173: .................. +173: ---------------------------------------------------------------------- +173: Ran 18 tests in 3.143s +173: +173: OK +179: ..............[12:26:00] SMARTS Parse Error: syntax error while parsing: fiib +179: [12:26:00] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' +179: ....[12:26:00] ERROR: Problems encountered parsing data fields +179: [12:26:00] ERROR: moving to the beginning of the next molecule +179: [12:26:00] ERROR: Problems encountered parsing data fields +179: [12:26:00] ERROR: moving to the beginning of the next molecule +179: [12:26:00] Spurious data before the first property will be ignored +179: [12:26:00] Property will be truncated after the first blank line +179: [12:26:00] Property will be truncated after the first blank line +179: [12:26:00] Property will be truncated after the first blank line +179: [12:26:00] ERROR: Problems encountered parsing data fields +179: [12:26:00] ERROR: moving to the beginning of the next molecule +179: [12:26:00] ERROR: Problems encountered parsing data fields +179: [12:26:00] ERROR: moving to the beginning of the next molecule +179: [12:26:00] Spurious data before the first property will be ignored +179: [12:26:00] Property will be truncated after the first blank line +179: [12:26:00] Property will be truncated after the first blank line +179: [12:26:00] Property will be truncated after the first blank line +179: [12:26:00] ERROR: Problems encountered parsing data fields +179: [12:26:00] ERROR: moving to the beginning of the next molecule +179: [12:26:00] Property will be truncated after the first blank line +179: [12:26:00] ERROR: Problems encountered parsing data fields +179: [12:26:00] ERROR: moving to the beginning of the next molecule +179: [12:26:00] Property will be truncated after the first blank line +179: .[12:26:00] SMILES Parse Error: syntax error while parsing: fail +179: [12:26:00] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +179: [12:26:00] ERROR: Smiles parse error on line 2 +179: [12:26:00] ERROR: Cannot create molecule from : 'fail' +179: >>> This may result in an infinite loop. It should finish almost instantly +179: <<< OK, it finished. +179: ............[12:26:00] Explicit valence for atom # 1 C, 5, is greater than permitted +168/222 Test #173: pyRGroupDecomposition .................. Passed 4.45 sec test 180 Start 180: pyTestConformerWrap 180: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testConformer.py" 180: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 180: Test timeout computed to be: 1500 -179: ..............[03:17:55] SMARTS Parse Error: syntax error while parsing: fiib -179: [03:17:55] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib' -180: ...... -180: ---------------------------------------------------------------------- -180: Ran 6 tests in 0.009s -180: -180: OK -179: ....[03:17:55] ERROR: Problems encountered parsing data fields -179: [03:17:55] ERROR: moving to the beginning of the next molecule -179: [03:17:55] ERROR: Problems encountered parsing data fields -179: [03:17:55] ERROR: moving to the beginning of the next molecule -179: [03:17:55] Spurious data before the first property will be ignored -179: [03:17:55] Property will be truncated after the first blank line -179: [03:17:55] Property will be truncated after the first blank line -179: [03:17:55] Property will be truncated after the first blank line -179: [03:17:55] ERROR: Problems encountered parsing data fields -179: [03:17:55] ERROR: moving to the beginning of the next molecule -179: [03:17:55] ERROR: Problems encountered parsing data fields -179: [03:17:55] ERROR: moving to the beginning of the next molecule -179: [03:17:55] Spurious data before the first property will be ignored -179: [03:17:55] Property will be truncated after the first blank line -179: [03:17:55] Property will be truncated after the first blank line -179: [03:17:55] Property will be truncated after the first blank line -179: [03:17:55] ERROR: Problems encountered parsing data fields -179: [03:17:55] ERROR: moving to the beginning of the next molecule -179: [03:17:55] Property will be truncated after the first blank line -179: [03:17:55] ERROR: Problems encountered parsing data fields -179: [03:17:55] ERROR: moving to the beginning of the next molecule -179: [03:17:55] Property will be truncated after the first blank line -179: .[03:17:55] SMILES Parse Error: syntax error while parsing: fail -179: [03:17:55] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -179: [03:17:55] ERROR: Smiles parse error on line 2 -179: [03:17:55] ERROR: Cannot create molecule from : 'fail' -179: >>> This may result in an infinite loop. It should finish almost instantly -179: <<< OK, it finished. -179: ............[03:17:55] Explicit valence for atom # 1 C, 5, is greater than permitted -169/222 Test #180: pyTestConformerWrap .................... Passed 0.44 sec -test 181 - Start 181: pyTestTrajectory - -181: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testTrajectory.py" -181: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -181: Test timeout computed to be: 1500 -179: ............[03:17:55] non-ring atom 0 marked aromatic -179: [03:17:55] non-ring atom 0 marked aromatic -179: [03:17:55] +179: ............[12:26:00] non-ring atom 0 marked aromatic +179: [12:26:00] non-ring atom 0 marked aromatic +179: [12:26:00] 179: 179: **** 179: Range Error @@ -23990,9 +23989,9 @@ 179: Failed Expression: 12 < 6 179: **** 179: -179: [03:17:55] non-ring atom 0 marked aromatic -179: [03:17:55] non-ring atom 0 marked aromatic -179: [03:17:55] +179: [12:26:00] non-ring atom 0 marked aromatic +179: [12:26:00] non-ring atom 0 marked aromatic +179: [12:26:00] 179: 179: **** 179: Range Error @@ -24001,12 +24000,57 @@ 179: Failed Expression: 12 < 6 179: **** 179: -179: ...............[03:17:55] 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. -179: [03:17:55] 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. -179: ..............[03:17:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -179: [03:17:56] Explicit valence for atom # 1 C, 5, is greater than permitted -170: bulk, no symmetry -181: [03:17:56] +179: ...............[12:26:00] 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. +179: [12:26:00] 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. +179: ..............[12:26:00] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +179: [12:26:00] Explicit valence for atom # 1 C, 5, is greater than permitted +134: ......[12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: .[12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: .[12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: [12:26:00] Molecule does not have explicit Hs. Consider calling AddHs() +134: . +134: ---------------------------------------------------------------------- +134: Ran 19 tests in 50.969s +134: +134: OK +169/222 Test #134: pyDistGeomHelpers ...................... Passed 52.00 sec +test 181 + Start 181: pyTestTrajectory + +181: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testTrajectory.py" +181: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +181: Test timeout computed to be: 1500 +180: ...... +180: ---------------------------------------------------------------------- +180: Ran 6 tests in 0.024s +180: +180: OK +170/222 Test #180: pyTestConformerWrap .................... Passed 1.15 sec +test 182 + Start 182: pyTestSGroups + +182: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testSGroups.py" +182: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap +182: Test timeout computed to be: 1500 +170: bulk +181: [12:26:01] 181: 181: **** 181: Pre-condition Violation @@ -24015,7 +24059,7 @@ 181: Failed Expression: from < static_cast(size()) 181: **** 181: -181: .[03:17:56] +181: .[12:26:01] 181: 181: **** 181: Pre-condition Violation @@ -24024,7 +24068,13 @@ 181: Failed Expression: from < static_cast(size()) 181: **** 181: -181: .[03:17:56] +182: ............. +182: ---------------------------------------------------------------------- +182: Ran 13 tests in 0.055s +182: +182: OK +182: Testing SubstanceGroups wrapper +181: .[12:26:02] 181: 181: **** 181: Range Error @@ -24033,7 +24083,7 @@ 181: Failed Expression: 0 < 0 181: **** 181: -181: .[03:17:56] +181: .[12:26:02] 181: 181: **** 181: Pre-condition Violation @@ -24042,7 +24092,7 @@ 181: Failed Expression: traj.dimension() == 3 181: **** 181: -181: ..[03:17:56] +181: ..[12:26:02] 181: 181: **** 181: Pre-condition Violation @@ -24051,7 +24101,7 @@ 181: Failed Expression: traj.dimension() == 3 181: **** 181: -181: .[03:17:56] +181: .[12:26:02] 181: 181: **** 181: Pre-condition Violation @@ -24060,7 +24110,7 @@ 181: Failed Expression: d_pos 181: **** 181: -181: [03:17:56] +181: [12:26:02] 181: 181: **** 181: Pre-condition Violation @@ -24069,7 +24119,7 @@ 181: Failed Expression: d_trajectory 181: **** 181: -181: .[03:17:56] +181: .[12:26:02] 181: 181: **** 181: Range Error @@ -24078,7 +24128,7 @@ 181: Failed Expression: 5 < 5 181: **** 181: -181: [03:17:56] +181: [12:26:02] 181: 181: **** 181: Range Error @@ -24087,7 +24137,7 @@ 181: Failed Expression: 10 < 10 181: **** 181: -181: .[03:17:56] +181: .[12:26:02] 181: 181: **** 181: Range Error @@ -24096,7 +24146,7 @@ 181: Failed Expression: 5 < 5 181: **** 181: -181: [03:17:56] +181: [12:26:02] 181: 181: **** 181: Pre-condition Violation @@ -24105,7 +24155,7 @@ 181: Failed Expression: d_trajectory->dimension() == 2 181: **** 181: -181: [03:17:56] +181: [12:26:02] 181: 181: **** 181: Pre-condition Violation @@ -24116,60 +24166,53 @@ 181: 181: . 181: ---------------------------------------------------------------------- -181: Ran 9 tests in 0.319s +181: Ran 9 tests in 0.512s 181: 181: OK 181: Testing Trajectory wrapper -170: [03:17:56] Relabelling existing label -170/222 Test #181: pyTestTrajectory ....................... Passed 0.88 sec -test 182 - Start 182: pyTestSGroups - -182: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testSGroups.py" -182: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap -182: Test timeout computed to be: 1500 -170: Best mapping -182: ............. -182: ---------------------------------------------------------------------- -182: Ran 13 tests in 0.014s -182: -182: OK -182: Testing SubstanceGroups wrapper -171/222 Test #170: testRGroupDecomp ....................... Passed 5.00 sec +171/222 Test #182: pyTestSGroups .......................... Passed 1.00 sec test 183 Start 183: pyTestThreads 183: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testThreads.py" 183: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 183: Test timeout computed to be: 1500 -172/222 Test #182: pyTestSGroups .......................... Passed 0.31 sec +172/222 Test #181: pyTestTrajectory ....................... Passed 1.54 sec test 184 Start 184: pyTestMultithreadedMolSupplier 184: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 184: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 184: Test timeout computed to be: 1500 -167: [03:17:57] ------------------------------------- -167: [03:17:57] Results do not depend on numThreads (all same) 184: .s. 184: ---------------------------------------------------------------------- -184: Ran 3 tests in 0.138s +184: Ran 3 tests in 0.347s 184: 184: OK (skipped=1) 184: Testing Smiles and SD MultithreadedMolSupplier -167: [03:17:57] ------------------------------------- -167: [03:17:57] testTautomerQueries -167: [03:17:57] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -167: [03:17:57] ------------------------------------- -167: [03:17:57] github3881 recursive smarts with rings -173/222 Test #167: substructLibraryTest ................... Passed 10.08 sec +173/222 Test #184: pyTestMultithreadedMolSupplier ......... Passed 1.26 sec test 185 Start 185: pyTestPropertyLists 185: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testPropertyLists.py" 185: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Wrap 185: Test timeout computed to be: 1500 -174/222 Test #184: pyTestMultithreadedMolSupplier ......... Passed 0.44 sec +170: bulk, no symmetry +185: [12:26:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +185: [12:26:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +185: [12:26:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +185: .[12:26:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +185: [12:26:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +185: [12:26:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +185: ...[12:26:04] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. +185: [12:26:04] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. +185: [12:26:04] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. +185: . +185: ---------------------------------------------------------------------- +185: Ran 5 tests in 0.017s +185: +185: OK +174/222 Test #185: pyTestPropertyLists .................... Passed 0.69 sec test 186 Start 186: pyCDXMLTest @@ -24178,125 +24221,112 @@ 186: Test timeout computed to be: 1500 186: . 186: ---------------------------------------------------------------------- -186: Ran 1 test in 0.006s +186: Ran 1 test in 0.027s 186: 186: OK -175/222 Test #186: pyCDXMLTest ............................ Passed 0.35 sec +175/222 Test #186: pyCDXMLTest ............................ Passed 0.79 sec test 187 Start 187: molStandardizeTest 187: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest 187: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 187: Test timeout computed to be: 1500 -185: [03:17:58] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -185: [03:17:58] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -185: [03:17:58] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -185: .[03:17:58] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -185: [03:17:58] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -185: [03:17:58] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -185: ...[03:17:58] Value [?] for property atom.iprop.PartiallyMissingInt of atom 0 can not be parsed. Ignoring it. -185: [03:17:58] Value ? for property atom.iprop.PartiallyMissingInt of atom 3 can not be parsed. Ignoring it. -185: [03:17:58] Value $$$$ for property atom.iprop.PartiallyMissingInt of atom 4 can not be parsed. Ignoring it. -185: . -185: ---------------------------------------------------------------------- -185: Ran 5 tests in 0.029s -185: -185: OK -176/222 Test #185: pyTestPropertyLists .................... Passed 0.60 sec +170: [12:26:05] Relabelling existing label +170: Best mapping +176/222 Test #170: testRGroupDecomp ....................... Passed 15.76 sec test 188 Start 188: molNormalizeTest 188: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest 188: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 188: Test timeout computed to be: 1500 -188: [03:17:58] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -188: [03:17:58] Initializing Normalizer -188: [03:17:58] Running Normalizer -188: [03:17:58] Rule applied: BrokenazidetoN=N+=N- -188: [03:17:58] Initializing Normalizer -188: [03:17:58] Running Normalizer -188: [03:17:58] Initializing Normalizer -188: [03:17:58] Running Normalizer -177/222 Test #188: molNormalizeTest ....................... Passed 0.14 sec +188: [12:26:06] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +188: [12:26:07] Initializing Normalizer +188: [12:26:07] Running Normalizer +188: [12:26:07] Rule applied: BrokenazidetoN=N+=N- +188: [12:26:07] Initializing Normalizer +188: [12:26:07] Running Normalizer +188: [12:26:07] Initializing Normalizer +188: [12:26:07] Running Normalizer +177/222 Test #188: molNormalizeTest ....................... Passed 0.35 sec test 189 Start 189: molValidateTest 189: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest 189: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 189: Test timeout computed to be: 1500 -178/222 Test #189: molValidateTest ........................ Passed 0.08 sec +178/222 Test #189: molValidateTest ........................ Passed 0.14 sec test 190 Start 190: molChargeTest 190: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest 190: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 190: Test timeout computed to be: 1500 -179/222 Test #190: molChargeTest .......................... Passed 0.12 sec +179/222 Test #187: molStandardizeTest ..................... Passed 2.41 sec test 191 Start 191: molTautomerTest 191: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest 191: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 191: Test timeout computed to be: 1500 -180/222 Test #187: molStandardizeTest ..................... Passed 0.62 sec +180/222 Test #190: molChargeTest .......................... Passed 0.27 sec test 192 Start 192: molStandardizeSmallTest 192: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest 192: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 192: Test timeout computed to be: 1500 -181/222 Test #192: molStandardizeSmallTest ................ Passed 0.03 sec +181/222 Test #192: molStandardizeSmallTest ................ Passed 0.15 sec test 193 Start 193: molFragmentTest 193: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest 193: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 193: Test timeout computed to be: 1500 -193: [03:17:58] SMARTS Parse Error: syntax error while parsing: [Cl -193: [03:17:58] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -182/222 Test #193: molFragmentTest ........................ Passed 0.04 sec +193: [12:26:07] SMARTS Parse Error: syntax error while parsing: [Cl +193: [12:26:07] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +182/222 Test #193: molFragmentTest ........................ Passed 0.14 sec test 194 Start 194: molStandardizeCatchTest 194: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest 194: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize 194: Test timeout computed to be: 1500 -194: Randomness seeded to: 188209996 +194: Randomness seeded to: 3778295808 194: * - * - * - * m1 194: * - * - * - * m2 194: * - * - * - * m1 194: * - * - * - * m2 -194: [03:17:58] Can't kekulize mol. Unkekulized atoms: 3 7 -194: [03:17:58] Can't kekulize mol. Unkekulized atoms: 3 8 -194: [03:17:58] Can't kekulize mol. Unkekulized atoms: 2 3 4 -191: [03:17:59] Tautomer enumeration stopped at 292 tautomers: max transforms reached -191: [03:17:59] Tautomer enumeration stopped at 292 tautomers: max transforms reached -191: [03:17:59] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -191: [03:17:59] Tautomer enumeration stopped at 86 tautomers: canceled +194: [12:26:08] Can't kekulize mol. Unkekulized atoms: 3 7 +194: [12:26:08] Can't kekulize mol. Unkekulized atoms: 3 8 +194: [12:26:08] Can't kekulize mol. Unkekulized atoms: 2 3 4 +191: [12:26:08] Tautomer enumeration stopped at 292 tautomers: max transforms reached +191: [12:26:09] Tautomer enumeration stopped at 292 tautomers: max transforms reached +191: [12:26:10] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +191: [12:26:10] Tautomer enumeration stopped at 28 tautomers: canceled 191: Enumeration was canceled due to timeout (50 ms) 191: 375 191: Enumeration has completed -29: [03:18:00] Finished -29: [03:18:00] ------------------------------------- -29: [03:18:00] Test github1843: RWMol.clear() should not destroy ring pointer. -29: [03:18:00] Finished -183/222 Test #29: graphmolTest1 .......................... Passed 31.01 sec -test 195 - Start 195: pyMolStandardize - -195: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap -195: Test timeout computed to be: 1500 -191: [03:18:00] Tautomer enumeration stopped at 126 tautomers: canceled -191: CN=c1cc[nH]cn1 -191: CN=c1ccnc[nH]1 -191: CNc1ccncn1 -191: res: CNc1ccncn1 -191: CN=c1cccc[nH]1 -191: CNc1ccccn1 -191: res: CNc1ccccn1 -179: ...........................[03:18:00] unable to set wavy bonds for double bonds: 3 -179: .........[03:18:00] +169: ......[12:26:11] +169: +169: **** +169: Pre-condition Violation +169: RingInfo not initialized +169: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp +169: Failed Expression: df_init +169: **** +169: +169: [12:26:11] +169: +169: **** +169: Pre-condition Violation +169: RingInfo not initialized +169: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp +169: Failed Expression: df_init +169: **** +169: +179: ...........................[12:26:12] unable to set wavy bonds for double bonds: 3 +179: .........[12:26:12] 179: 179: **** 179: Range Error @@ -24305,38 +24335,55 @@ 179: Failed Expression: 6 < 5 179: **** 179: -184/222 Test #191: molTautomerTest ........................ Passed 2.03 sec +191: CN=c1cc[nH]cn1 +191: CN=c1ccnc[nH]1 +191: CNc1ccncn1 +191: res: CNc1ccncn1 +191: CN=c1cccc[nH]1 +191: CNc1ccccn1 +191: res: CNc1ccccn1 +183/222 Test #191: molTautomerTest ........................ Passed 5.55 sec +test 195 + Start 195: pyMolStandardize + +195: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolStandardize/Wrap +195: Test timeout computed to be: 1500 +195: .....[12:26:14] Tautomer enumeration stopped at 292 tautomers: max transforms reached +195: [12:26:14] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +195: .[12:26:15] Tautomer enumeration stopped at 23 tautomers: canceled +195: Enumeration was canceled due to timeout (50 ms) +179: ...................[12:26:15] Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:15] Explicit valence for atom # 6 F, 2, is greater than permitted +179: [12:26:15] Can't kekulize mol. Unkekulized atoms: 3 4 5 +179: ...............[12:26:15] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +194: =============================================================================== +194: All tests passed (18691 assertions in 41 test cases) +194: +184/222 Test #194: molStandardizeCatchTest ................ Passed 9.09 sec test 196 Start 196: testScaffoldNetwork 196: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 196: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork 196: Test timeout computed to be: 1500 -195: .....[03:18:00] Tautomer enumeration stopped at 292 tautomers: max transforms reached -195: [03:18:00] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -195: .[03:18:00] Tautomer enumeration stopped at 93 tautomers: canceled -195: Enumeration was canceled due to timeout (50 ms) 195: Enumeration has completed -195: [03:18:01] Tautomer enumeration stopped at 85 tautomers: canceled -179: ...................[03:18:01] Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:01] Explicit valence for atom # 6 F, 2, is greater than permitted -179: [03:18:01] Can't kekulize mol. Unkekulized atoms: 3 4 5 -196: Randomness seeded to: 3237383298 -196: =============================================================================== -196: All tests passed (269 assertions in 19 test cases) -196: -185/222 Test #196: testScaffoldNetwork .................... Passed 1.18 sec +195: [12:26:17] Tautomer enumeration stopped at 40 tautomers: canceled +195: ....................[12:26:18] Explicit valence for atom # 1 O, 3, is greater than permitted +185/222 Test #183: pyTestThreads .......................... Passed 16.51 sec test 197 Start 197: pyScaffoldNetwork 197: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 197: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap 197: Test timeout computed to be: 1500 -179: ...............[03:18:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -194: =============================================================================== -194: All tests passed (18691 assertions in 41 test cases) -194: -186/222 Test #194: molStandardizeCatchTest ................ Passed 3.22 sec +195: . +195: ---------------------------------------------------------------------- +195: Ran 27 tests in 5.342s +195: +195: OK +195: done +186/222 Test #195: pyMolStandardize ....................... Passed 6.07 sec test 198 Start 198: pyScaffoldNetworkPickling @@ -24345,85 +24392,87 @@ 198: Test timeout computed to be: 1500 197: ....... 197: ---------------------------------------------------------------------- -197: Ran 7 tests in 0.024s +197: Ran 7 tests in 0.097s 197: 197: OK -187/222 Test #197: pyScaffoldNetwork ...................... Passed 0.30 sec +196: Randomness seeded to: 1273396714 +196: =============================================================================== +196: All tests passed (269 assertions in 19 test cases) +196: +187/222 Test #196: testScaffoldNetwork .................... Passed 2.90 sec test 199 Start 199: testMolEnumerator 199: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 199: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator 199: Test timeout computed to be: 1500 -198: . -198: ---------------------------------------------------------------------- -198: Ran 1 test in 0.008s -198: -198: OK -199: Randomness seeded to: 4151315711 -199: [03:18:02] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -195: ....................[03:18:02] Explicit valence for atom # 1 O, 3, is greater than permitted -199: =============================================================================== -199: All tests passed (321 assertions in 16 test cases) -199: -195: . -195: ---------------------------------------------------------------------- -195: Ran 27 tests in 1.730s -195: -195: OK -195: done -188/222 Test #199: testMolEnumerator ...................... Passed 0.05 sec +188/222 Test #197: pyScaffoldNetwork ...................... Passed 1.12 sec test 200 Start 200: pyMolEnumerator 200: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 200: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 200: Test timeout computed to be: 1500 -189/222 Test #198: pyScaffoldNetworkPickling .............. Passed 0.27 sec +199: Randomness seeded to: 3214432258 +199: [12:26:20] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +199: =============================================================================== +199: All tests passed (321 assertions in 16 test cases) +199: +189/222 Test #199: testMolEnumerator ...................... Passed 0.17 sec test 201 Start 201: testAbbreviations 201: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 201: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations 201: Test timeout computed to be: 1500 -190/222 Test #195: pyMolStandardize ....................... Passed 2.06 sec +201: Randomness seeded to: 803607618 +201: [12:26:20] SMARTS Parse Error: syntax error while parsing: *fail +201: [12:26:20] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +201: [12:26:20] no suitable SubstanceGroups found +201: =============================================================================== +201: All tests passed (195 assertions in 12 test cases) +201: +190/222 Test #201: testAbbreviations ...................... Passed 0.09 sec test 202 Start 202: pyAbbreviations 202: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 202: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/Abbreviations/Wrap 202: Test timeout computed to be: 1500 -201: Randomness seeded to: 3615859551 -201: [03:18:02] SMARTS Parse Error: syntax error while parsing: *fail -201: [03:18:02] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -201: [03:18:02] no suitable SubstanceGroups found -201: =============================================================================== -201: All tests passed (195 assertions in 12 test cases) -201: -191/222 Test #201: testAbbreviations ...................... Passed 0.06 sec +198: . +198: ---------------------------------------------------------------------- +198: Ran 1 test in 0.040s +198: +198: OK +191/222 Test #198: pyScaffoldNetworkPickling .............. Passed 1.27 sec test 203 Start 203: generalizedSubstructCatch 203: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 203: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct 203: Test timeout computed to be: 1500 -203: Randomness seeded to: 216681501 +200: ... +200: ---------------------------------------------------------------------- +200: Ran 3 tests in 0.044s +200: +200: OK +202: ....... +202: ---------------------------------------------------------------------- +202: Ran 7 tests in 0.077s +202: +202: OK +203: Randomness seeded to: 3888909269 203: =============================================================================== 203: All tests passed (180 assertions in 10 test cases) 203: -192/222 Test #203: generalizedSubstructCatch .............. Passed 0.15 sec +192/222 Test #203: generalizedSubstructCatch .............. Passed 0.59 sec test 204 Start 204: pyGeneralizedSubstruct 204: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 204: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 204: Test timeout computed to be: 1500 -202: ....... -202: ---------------------------------------------------------------------- -202: Ran 7 tests in 0.012s -202: -202: OK -193/222 Test #202: pyAbbreviations ........................ Passed 0.27 sec +193/222 Test #200: pyMolEnumerator ........................ Passed 1.11 sec test 205 Start 205: testQuery @@ -24447,7 +24496,7 @@ 205: XOr 205: pointer and copy foo 205: Set2 -194/222 Test #205: testQuery .............................. Passed 0.01 sec +194/222 Test #205: testQuery .............................. Passed 0.02 sec test 206 Start 206: testMatCalc @@ -24499,70 +24548,71 @@ 206: 9.49496e+07 206: 2.25618e+08 206: 1.30219e+08 -195/222 Test #206: testMatCalc ............................ Passed 0.00 sec +195/222 Test #206: testMatCalc ............................ Passed 0.02 sec test 207 Start 207: pyMatCalc 207: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 207: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 207: Test timeout computed to be: 1500 -200: ... -200: ---------------------------------------------------------------------- -200: Ran 3 tests in 0.008s -200: -200: OK -196/222 Test #200: pyMolEnumerator ........................ Passed 0.45 sec +196/222 Test #202: pyAbbreviations ........................ Passed 1.04 sec test 208 Start 208: testSimDivPickers 208: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers/testSimDivPickers 208: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers 208: Test timeout computed to be: 1500 -208: [03:18:02] ------------------------------------- -208: [03:18:02] Testing github issue 1421: MaxMinPicker picking non-existent element. -208: [03:18:02] Done -208: [03:18:02] ------------------------------------- -208: [03:18:02] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -208: [03:18:02] Done -197/222 Test #208: testSimDivPickers ...................... Passed 0.01 sec +208: [12:26:21] ------------------------------------- +208: [12:26:21] Testing github issue 1421: MaxMinPicker picking non-existent element. +208: [12:26:21] Done +208: [12:26:21] ------------------------------------- +208: [12:26:21] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +208: [12:26:21] Done +197/222 Test #208: testSimDivPickers ...................... Passed 0.02 sec test 209 Start 209: pickersTestsCatch 209: Test command: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers/pickersTestsCatch 209: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers 209: Test timeout computed to be: 1500 -209: Randomness seeded to: 3005667376 -209: =============================================================================== -209: All tests passed (21267 assertions in 1 test case) -209: -198/222 Test #209: pickersTestsCatch ...................... Passed 0.05 sec +136: --------------------------------- +136: test getO3AForProbeConfs +136: +136: *********************************************************** +198/222 Test #136: testO3AAlign ........................... Passed 71.06 sec test 210 Start 210: pySimDivPickers 210: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/testPickers.py" 210: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/SimDivPickers/Wrap 210: Test timeout computed to be: 1500 -204: ....... -204: ---------------------------------------------------------------------- -204: Ran 7 tests in 0.097s -204: -204: OK -199/222 Test #204: pyGeneralizedSubstruct ................. Passed 0.40 sec +209: Randomness seeded to: 1584165326 +209: =============================================================================== +209: All tests passed (21267 assertions in 1 test case) +209: +199/222 Test #209: pickersTestsCatch ...................... Passed 0.23 sec test 211 Start 211: pyRanker 211: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/testRanker.py" 211: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ML/InfoTheory/Wrap 211: Test timeout computed to be: 1500 -210: [03:18:02] the useCache argument is deprecated and ignored -210: ...[03:18:02] the useCache argument is deprecated and ignored -210: [03:18:02] the useCache argument is deprecated and ignored -210: .[03:18:02] the useCache argument is deprecated and ignored -136: --------------------------------- -136: test getO3AForProbeConfs -136: -136: *********************************************************** -200/222 Test #136: testO3AAlign ........................... Passed 26.77 sec +211: ..[12:26:22] +211: +211: **** +211: Invariant Violation +211: Can't rank more bits than the ensemble size +211: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp +211: Failed Expression: num <= dp_maskBits->getNumOnBits() +211: **** +211: +211: ... +211: ---------------------------------------------------------------------- +211: Ran 5 tests in 0.049s +211: +211: OK +210: [12:26:22] the useCache argument is deprecated and ignored +200/222 Test #211: pyRanker ............................... Passed 1.01 sec test 212 Start 212: testChemicalFeatures @@ -24572,372 +24622,306 @@ 212: ----------------------------------------- 212: Test1 212: Done -201/222 Test #212: testChemicalFeatures ................... Passed 0.01 sec +201/222 Test #212: testChemicalFeatures ................... Passed 0.02 sec test 213 Start 213: pyFeatures 213: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/testFeatures.py" 213: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Code/ChemicalFeatures/Wrap 213: Test timeout computed to be: 1500 -211: ..[03:18:03] -211: -211: **** -211: Invariant Violation -211: Can't rank more bits than the ensemble size -211: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp -211: Failed Expression: num <= dp_maskBits->getNumOnBits() -211: **** -211: -211: ... -211: ---------------------------------------------------------------------- -211: Ran 5 tests in 0.029s -211: -211: OK -207: ..... -207: ---------------------------------------------------------------------- -207: Ran 5 tests in 0.438s -207: -207: OK -202/222 Test #211: pyRanker ............................... Passed 0.50 sec +204: ....... +204: ---------------------------------------------------------------------- +204: Ran 7 tests in 0.516s +204: +204: OK +202/222 Test #204: pyGeneralizedSubstruct ................. Passed 1.87 sec test 214 Start 214: pythonTestDbCLI 214: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/Projects" 214: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/Projects 214: Test timeout computed to be: 1500 -203/222 Test #207: pyMatCalc .............................. Passed 0.81 sec -test 215 - Start 215: pythonTestDirRoot - -215: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit" -215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit -215: Test timeout computed to be: 1500 +210: ...[12:26:23] the useCache argument is deprecated and ignored +210: [12:26:23] the useCache argument is deprecated and ignored +210: .[12:26:23] the useCache argument is deprecated and ignored +179: ..[12:26:23] +179: +179: **** +179: Pre-condition Violation +179: no owner +179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +179: Failed Expression: dp_mol +179: **** +179: +179: [12:26:23] +179: +179: **** +179: Pre-condition Violation +179: no owner +179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +179: Failed Expression: dp_mol +179: **** +179: +179: [12:26:23] +179: +179: **** +179: Pre-condition Violation +179: no owner +179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +179: Failed Expression: dp_mol +179: **** +179: +179: [12:26:23] +179: +179: **** +179: Pre-condition Violation +179: no owner +179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +179: Failed Expression: dp_mol +179: **** +179: +179: [12:26:23] +179: +179: **** +179: Pre-condition Violation +179: no owner +179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +179: Failed Expression: dp_mol +179: **** +179: +179: .....[12:26:23] +179: +179: **** +179: Range Error +179: atomIdx1 +179: Violation occurred on line 377 in file ./Code/GraphMol/RWMol.cpp +179: Failed Expression: 0 < 0 +179: **** +179: 213: .. 213: ---------------------------------------------------------------------- 213: Ran 2 tests in 0.001s 213: 213: OK 213: Testing ChemicalFeatures Wrapper code: -204/222 Test #213: pyFeatures ............................. Passed 0.28 sec +179: ......[12:26:23] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +179: [12:26:23] ERROR: Smiles parse error on line 0 +179: [12:26:23] ERROR: Cannot create molecule from : 'c1ccccc' +179: [12:26:23] SMILES Parse Error: extra open parentheses for input: 'C(C' +179: [12:26:23] ERROR: Smiles parse error on line 3 +179: [12:26:23] ERROR: Cannot create molecule from : 'C(C' +179: [12:26:23] Explicit valence for atom # 1 C, 5, is greater than permitted +179: [12:26:23] ERROR: Could not sanitize molecule on line 6 +179: [12:26:23] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +179: [12:26:23] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +179: [12:26:23] ERROR: Smiles parse error on line 0 +179: [12:26:23] ERROR: Cannot create molecule from : 'c1ccccc' +179: [12:26:23] SMILES Parse Error: extra open parentheses for input: 'C(C' +179: [12:26:23] ERROR: Smiles parse error on line 3 +179: [12:26:23] ERROR: Cannot create molecule from : 'C(C' +179: [12:26:23] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' +179: [12:26:23] ERROR: Smiles parse error on line 6 +179: [12:26:23] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' +179: [12:26:23] Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:23] ERROR: Could not sanitize molecule ending on line 21 +179: [12:26:23] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:23] ERROR: EOF hit while reading atoms +179: [12:26:23] ERROR: moving to the beginning of the next molecule +179: [12:26:23] Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:23] ERROR: Could not sanitize molecule ending on line 21 +179: [12:26:23] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:23] ERROR: EOF hit while reading atoms +179: [12:26:23] ERROR: moving to the beginning of the next molecule +179: ....[12:26:23] +179: +179: **** +179: Pre-condition Violation +179: RingInfo not initialized +179: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp +179: Failed Expression: df_init +179: **** +179: +179: ..........[12:26:23] +179: +179: **** +179: Range Error +179: idx +179: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp +179: Failed Expression: 3 < 1 +179: **** +179: +179: ..[12:26:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +207: ..... +207: ---------------------------------------------------------------------- +207: Ran 5 tests in 1.410s +207: +207: OK +203/222 Test #213: pyFeatures ............................. Passed 1.03 sec +test 215 + Start 215: pythonTestDirRoot + +215: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit" +215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit +215: Test timeout computed to be: 1500 +179: ..........................[12:26:23] SMILES Parse Error: unclosed ring for input: 'C1CC' +204/222 Test #207: pyMatCalc .............................. Passed 2.54 sec test 216 Start 216: pythonTestDirML 216: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/ML/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/ML" 216: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit 216: Test timeout computed to be: 1500 -210: ....... -210: ---------------------------------------------------------------------- -210: Ran 11 tests in 0.669s -210: -210: OK +179: ......[12:26:23] WARNING: not removing hydrogen atom without neighbors +179: [12:26:23] WARNING: not removing hydrogen atom with dummy atom neighbors +179: [12:26:23] WARNING: not removing hydrogen atom with wedged bond +179: [12:26:23] WARNING: not removing hydrogen atom without neighbors +179: [12:26:23] WARNING: not removing hydrogen atom with dummy atom neighbors 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML import BuildComposite -205/222 Test #210: pySimDivPickers ........................ Passed 0.97 sec +179: .....[12:26:24] Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 +179: .[12:26:24] Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:24] Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:24] Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:24] Explicit valence for atom # 1 F, 2, is greater than permitted +179: [12:26:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 +179: [12:26:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 +179: [12:26:24] Can't kekulize mol. Unkekulized atoms: 0 1 2 +179: ..........[12:26:24] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +179: [12:26:24] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +179: .[12:26:24] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname +179: [12:26:24] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' +179: ..[12:26:24] SMILES Parse Error: syntax error while parsing: error +179: [12:26:24] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' +179: [12:26:24] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' +179: [12:26:24] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' +179: [12:26:24] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' +179: ................[12:26:24] SMILES Parse Error: syntax error while parsing: garbage_0 +179: [12:26:24] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' +179: [12:26:24] SMILES Parse Error: syntax error while parsing: garbage_2 +179: [12:26:24] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' +179: [12:26:24] SMILES Parse Error: syntax error while parsing: garbage_4 +179: [12:26:24] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' +179: .......... +179: ---------------------------------------------------------------------- +179: Ran 248 tests in 24.541s +179: +179: OK +179: 151 +179: supplier: +179: supplier: +179: supplier: +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: refCompos = pickle.load(pklF) +205/222 Test #179: pyGraphMolWrap ......................... Passed 25.86 sec test 217 Start 217: pythonTestDirDataStructs 217: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs" 217: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit 217: Test timeout computed to be: 1500 -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: refCompos = pickle.load(pklF) -217: ....... -217: ---------------------------------------------------------------------- -217: Ran 7 tests in 0.012s -217: -217: OK -216: ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: refCompos = pickle.load(pklFile) -216: . -216: ---------------------------------------------------------------------- -216: Ran 6 tests in 0.234s -216: -216: OK -214: [03:18:04] INFO: Reading molecules and constructing molecular database. -214: -214: [03:18:04] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -214: -214: [03:18:04] INFO: Processing 10 molecules -214: -214: [03:18:04] INFO: Generating fingerprints and descriptors: -214: -214: [03:18:04] INFO: Finished. -214: -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: from rdkit.ML import ScreenComposite -217: .................................. -217: ---------------------------------------------------------------------- -217: Ran 34 tests in 0.007s -217: -217: OK 215: ......................... 215: ---------------------------------------------------------------------- -215: Ran 25 tests in 0.980s +215: Ran 25 tests in 1.202s 215: 215: OK -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: compos = pickle.load(pklF) -206/222 Test #215: pythonTestDirRoot ...................... Passed 1.17 sec +206/222 Test #215: pythonTestDirRoot ...................... Passed 2.02 sec test 218 Start 218: pythonTestDirDbase 218: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase" 218: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit 218: Test timeout computed to be: 1500 -216: ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: compos = pickle.load(pklF) -216: .......... +216: ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: refCompos = pickle.load(pklFile) +216: . 216: ---------------------------------------------------------------------- -216: Ran 12 tests in 0.113s +216: Ran 6 tests in 1.201s 216: 216: OK -217: ..... -217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.004s -217: -217: OK +210: ....... +210: ---------------------------------------------------------------------- +210: Ran 11 tests in 3.903s +210: +210: OK 218: .. 218: ---------------------------------------------------------------------- -218: Ran 2 tests in 0.017s +218: Ran 2 tests in 0.061s 218: 218: OK -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: from rdkit.ML import AnalyzeComposite -214: [03:18:04] INFO: Reading molecules and constructing molecular database. -214: -214: [03:18:04] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -214: -214: [03:18:04] INFO: Processing 163 molecules -214: -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] INFO: done 100 -214: -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -218: ........... -218: ---------------------------------------------------------------------- -218: Ran 11 tests in 0.029s -218: -218: OK -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:04] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: c1 = pickle.load(pklF) -214: [03:18:04] INFO: Generating fingerprints and descriptors: -214: 217: ....... 217: ---------------------------------------------------------------------- -217: Ran 7 tests in 0.001s +217: Ran 7 tests in 0.056s 217: 217: OK -216: . -216: ---------------------------------------------------------------------- -216: Ran 1 test in 0.055s -216: -216: OK -207/222 Test #217: pythonTestDirDataStructs ............... Passed 1.50 sec +207/222 Test #210: pySimDivPickers ........................ Passed 5.12 sec test 219 Start 219: pythonTestDirSimDivFilters 219: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters" 219: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit 219: Test timeout computed to be: 1500 -218: . +214: [12:26:26] INFO: Reading molecules and constructing molecular database. +214: +214: [12:26:26] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: +214: [12:26:26] INFO: Processing 10 molecules +214: +214: [12:26:26] INFO: Generating fingerprints and descriptors: +214: +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: from rdkit.ML import ScreenComposite +218: ........... 218: ---------------------------------------------------------------------- -218: Ran 1 test in 0.001s +218: Ran 11 tests in 0.064s 218: 218: OK -218: ............... +214: [12:26:26] INFO: Finished. +214: +218: . 218: ---------------------------------------------------------------------- -218: Ran 15 tests in 0.013s +218: Ran 1 test in 0.017s 218: 218: OK -218: ...... +217: .................................. +217: ---------------------------------------------------------------------- +217: Ran 34 tests in 0.016s +217: +217: OK +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: compos = pickle.load(pklF) +216: ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: compos = pickle.load(pklF) +216: .......... +216: ---------------------------------------------------------------------- +216: Ran 12 tests in 0.401s +216: +216: OK +218: ............... 218: ---------------------------------------------------------------------- -218: Ran 6 tests in 0.003s +218: Ran 15 tests in 0.050s 218: 218: OK -208/222 Test #218: pythonTestDirDbase ..................... Passed 1.10 sec +208/222 Test #219: pythonTestDirSimDivFilters ............. Passed 1.61 sec test 220 Start 220: pythonTestDirVLib 220: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/VLib" 220: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit 220: Test timeout computed to be: 1500 -216: ... -216: ---------------------------------------------------------------------- -216: Ran 3 tests in 0.001s -216: -216: OK -209/222 Test #219: pythonTestDirSimDivFilters ............. Passed 0.61 sec +217: ..... +217: ---------------------------------------------------------------------- +217: Ran 5 tests in 0.020s +217: +217: OK +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: from rdkit.ML import AnalyzeComposite +218: ...... +218: ---------------------------------------------------------------------- +218: Ran 6 tests in 0.003s +218: +218: OK +209/222 Test #218: pythonTestDirDbase ..................... Passed 3.21 sec test 221 Start 221: pythonTestSping @@ -24946,212 +24930,269 @@ 221: Test timeout computed to be: 1500 220: ............. 220: ---------------------------------------------------------------------- -220: Ran 13 tests in 0.008s +220: Ran 13 tests in 0.044s 220: 220: OK -216: ........ +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: c1 = pickle.load(pklF) +216: . 216: ---------------------------------------------------------------------- -216: Ran 8 tests in 0.005s +216: Ran 1 test in 0.131s 216: 216: OK -220: ........... -220: ---------------------------------------------------------------------- -220: Ran 11 tests in 0.063s -220: -220: OK -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: from rdkit.ML.Composite import Composite -210/222 Test #220: pythonTestDirVLib ...................... Passed 0.89 sec +217: ....... +217: ---------------------------------------------------------------------- +217: Ran 7 tests in 0.001s +217: +217: OK +214: [12:26:29] INFO: Reading molecules and constructing molecular database. +214: +214: [12:26:29] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: +214: [12:26:29] INFO: Processing 163 molecules +214: +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +210/222 Test #217: pythonTestDirDataStructs ............... Passed 5.08 sec test 222 Start 222: pythonTestDirChem 222: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Chem" "--buildType" "None" 222: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit/Chem 222: Test timeout computed to be: 1500 -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node -179: ..[03:18:06] -179: -179: **** -179: Pre-condition Violation -179: no owner -179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -179: Failed Expression: dp_mol -179: **** -179: -179: [03:18:06] -179: -179: **** -179: Pre-condition Violation -179: no owner -179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -179: Failed Expression: dp_mol -179: **** -179: -179: [03:18:06] -179: -179: **** -179: Pre-condition Violation -179: no owner -179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -179: Failed Expression: dp_mol -179: **** -179: -179: [03:18:06] -179: -179: **** -179: Pre-condition Violation -179: no owner -179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -179: Failed Expression: dp_mol -179: **** -179: -179: [03:18:06] -179: -179: **** -179: Pre-condition Violation -179: no owner -179: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -179: Failed Expression: dp_mol -179: **** -179: -179: .....[03:18:06] -179: -179: **** -179: Range Error -179: atomIdx1 -179: Violation occurred on line 377 in file ./Code/GraphMol/RWMol.cpp -179: Failed Expression: 0 < 0 -179: **** -179: -179: ......[03:18:06] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -179: [03:18:06] ERROR: Smiles parse error on line 0 -179: [03:18:06] ERROR: Cannot create molecule from : 'c1ccccc' -179: [03:18:06] SMILES Parse Error: extra open parentheses for input: 'C(C' -179: [03:18:06] ERROR: Smiles parse error on line 3 -179: [03:18:06] ERROR: Cannot create molecule from : 'C(C' -179: [03:18:06] Explicit valence for atom # 1 C, 5, is greater than permitted -179: [03:18:06] ERROR: Could not sanitize molecule on line 6 -179: [03:18:06] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -179: [03:18:06] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -179: [03:18:06] ERROR: Smiles parse error on line 0 -179: [03:18:06] ERROR: Cannot create molecule from : 'c1ccccc' -179: [03:18:06] SMILES Parse Error: extra open parentheses for input: 'C(C' -179: [03:18:06] ERROR: Smiles parse error on line 3 -179: [03:18:06] ERROR: Cannot create molecule from : 'C(C' -179: [03:18:06] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC' -179: [03:18:06] ERROR: Smiles parse error on line 6 -179: [03:18:06] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC' -179: [03:18:06] Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] ERROR: Could not sanitize molecule ending on line 21 -179: [03:18:06] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] ERROR: EOF hit while reading atoms -179: [03:18:06] ERROR: moving to the beginning of the next molecule -179: [03:18:06] Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] ERROR: Could not sanitize molecule ending on line 21 -179: [03:18:06] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] ERROR: EOF hit while reading atoms -179: [03:18:06] ERROR: moving to the beginning of the next molecule -179: ....[03:18:06] -179: -179: **** -179: Pre-condition Violation -179: RingInfo not initialized -179: Violation occurred on line 170 in file ./Code/GraphMol/RingInfo.cpp -179: Failed Expression: df_init -179: **** -179: -179: ..........[03:18:06] -179: -179: **** -179: Range Error -179: idx -179: Violation occurred on line 213 in file ./Code/GraphMol/ROMol.cpp -179: Failed Expression: 3 < 1 -179: **** -179: -179: ..[03:18:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] INFO: done 100 +214: +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:30] INFO: Generating fingerprints and descriptors: +214: +220: ........... +220: ---------------------------------------------------------------------- +220: Ran 11 tests in 0.192s +220: +220: OK +169: ............. +169: ---------------------------------------------------------------------- +169: Ran 19 tests in 40.993s +169: +169: OK +169: Testing atom rings +169: testing bond rings +169: searching atom rings +169: searching bond rings +169: done +216: ... +216: ---------------------------------------------------------------------- +216: Ran 3 tests in 0.001s +216: +216: OK +211/222 Test #169: pySubstructLibrary ..................... Passed 42.38 sec +212/222 Test #220: pythonTestDirVLib ...................... Passed 2.94 sec 221: .. 221: ---------------------------------------------------------------------- -221: Ran 2 tests in 0.359s +221: Ran 2 tests in 0.781s 221: 221: OK -216: .... +213/222 Test #221: pythonTestSping ........................ Passed 3.07 sec +216: ........ 216: ---------------------------------------------------------------------- -216: Ran 4 tests in 0.208s +216: Ran 8 tests in 0.000s 216: 216: OK -179: ..........................[03:18:06] SMILES Parse Error: unclosed ring for input: 'C1CC' -179: ......[03:18:06] WARNING: not removing hydrogen atom without neighbors -179: [03:18:06] WARNING: not removing hydrogen atom with dummy atom neighbors -179: [03:18:06] WARNING: not removing hydrogen atom with wedged bond -179: [03:18:06] WARNING: not removing hydrogen atom without neighbors -179: [03:18:06] WARNING: not removing hydrogen atom with dummy atom neighbors -179: .....[03:18:06] Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 -179: .[03:18:06] Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] Explicit valence for atom # 1 F, 2, is greater than permitted -179: [03:18:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 -179: [03:18:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 -179: [03:18:06] Can't kekulize mol. Unkekulized atoms: 0 1 2 -211/222 Test #221: pythonTestSping ........................ Passed 1.26 sec -179: ..........[03:18:06] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -179: [03:18:06] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -179: .[03:18:06] SMILES Parse Error: syntax error while parsing: CCC |$foo;;bar$| ourname -179: [03:18:06] SMILES Parse Error: Failed parsing SMILES 'CCC |$foo;;bar$| ourname' for input: 'CCC |$foo;;bar$| ourname' -179: ..[03:18:06] SMILES Parse Error: syntax error while parsing: error -179: [03:18:06] SMILES Parse Error: Failed parsing SMILES 'error' for input: 'error' -179: [03:18:06] SMILES Parse Error: Failed parsing SMILES 'd' for input: 'd' -179: [03:18:06] SMARTS Parse Error: Failed parsing SMARTS 'error' for input: 'error' -179: [03:18:06] SMARTS Parse Error: Failed parsing SMARTS 'd' for input: 'd' -179: ................[03:18:06] SMILES Parse Error: syntax error while parsing: garbage_0 -179: [03:18:06] SMILES Parse Error: Failed parsing SMILES 'garbage_0' for input: 'garbage_0' -179: [03:18:06] SMILES Parse Error: syntax error while parsing: garbage_2 -179: [03:18:06] SMILES Parse Error: Failed parsing SMILES 'garbage_2' for input: 'garbage_2' -179: [03:18:06] SMILES Parse Error: syntax error while parsing: garbage_4 -179: [03:18:06] SMILES Parse Error: Failed parsing SMILES 'garbage_4' for input: 'garbage_4' -179: .......... -179: ---------------------------------------------------------------------- -179: Ran 248 tests in 11.094s -179: -179: OK -179: 811 -179: supplier: -179: supplier: -179: supplier: -212/222 Test #179: pyGraphMolWrap ......................... Passed 11.63 sec +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: from rdkit.ML.Composite import Composite 222: ....... 222: ---------------------------------------------------------------------- -222: Ran 7 tests in 0.060s +222: Ran 7 tests in 0.315s 222: 222: OK -133: [03:18:07] UFFTYPER: Unrecognized atom type: S_6+6 (0) -133: [03:18:07] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -133: [03:18:07] UFFTYPER: Unrecognized charge state for atom: 0 -216: ..... +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node +29: [12:26:33] Finished +29: [12:26:33] ------------------------------------- +29: [12:26:33] Test github1843: RWMol.clear() should not destroy ring pointer. +29: [12:26:33] Finished +214/222 Test #29: graphmolTest1 .......................... Passed 99.70 sec +216: .... 216: ---------------------------------------------------------------------- -216: Ran 5 tests in 0.001s +216: Ran 4 tests in 0.895s 216: 216: OK 222: ...... 222: ---------------------------------------------------------------------- -222: Ran 6 tests in 0.023s +222: Ran 6 tests in 0.096s 222: 222: OK -133: =============================================================================== -133: All tests passed (448 assertions in 10 test cases) -133: -214: [03:18:07] INFO: Finished. -214: -213/222 Test #133: distGeomHelpersCatch ................... Passed 31.93 sec -216: ......... -216: ---------------------------------------------------------------------- -216: Ran 9 tests in 0.002s -216: -216: OK -222: ....[03:18:07] +222: ....[12:26:34] 222: 222: **** 222: Pre-condition Violation @@ -25162,391 +25203,61 @@ 222: 222: . 222: ---------------------------------------------------------------------- -222: Ran 5 tests in 0.006s +222: Ran 5 tests in 0.034s 222: 222: OK -214/222 Test #183: pyTestThreads .......................... Passed 10.61 sec -216: ............ +216: ..... 216: ---------------------------------------------------------------------- -216: Ran 12 tests in 0.001s +216: Ran 5 tests in 0.001s 216: 216: OK 222: .... 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.006s +222: Ran 4 tests in 0.023s 222: 222: OK -214: .[03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -169: ......[03:18:07] -169: -169: **** -169: Pre-condition Violation -169: RingInfo not initialized -169: Violation occurred on line 52 in file ./Code/GraphMol/RingInfo.cpp -169: Failed Expression: df_init -169: **** -169: -169: [03:18:07] -169: -169: **** -169: Pre-condition Violation -169: RingInfo not initialized -169: Violation occurred on line 129 in file ./Code/GraphMol/RingInfo.cpp -169: Failed Expression: df_init -169: **** -169: -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -216: ..... +216: ......... 216: ---------------------------------------------------------------------- -216: Ran 5 tests in 0.010s +216: Ran 9 tests in 0.002s 216: 216: OK -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 222: .. 222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.007s +222: Ran 2 tests in 0.035s 222: 222: OK -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +216: ............ +216: ---------------------------------------------------------------------- +216: Ran 12 tests in 0.001s +216: +216: OK 222: ...................... 222: ---------------------------------------------------------------------- -222: Ran 22 tests in 0.019s +222: Ran 22 tests in 0.083s 222: 222: OK -214: .[03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +216: ..... +216: ---------------------------------------------------------------------- +216: Ran 5 tests in 0.051s +216: +216: OK +222: .....s.................ss +222: ---------------------------------------------------------------------- +222: Ran 25 tests in 0.399s +222: +222: OK (skipped=3) 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import TreeUtils -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: . 216: ---------------------------------------------------------------------- -216: Ran 1 test in 0.000s +216: Ran 1 test in 0.017s 216: 216: OK -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: .....s.................ss +222: ..s 222: ---------------------------------------------------------------------- -222: Ran 25 tests in 0.074s +222: Ran 3 tests in 0.290s 222: -222: OK (skipped=3) +222: OK (skipped=1) 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTree.py:13: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import Tree 216: ...... @@ -25554,913 +25265,1233 @@ 216: Ran 6 tests in 0.001s 216: 216: OK +214: [12:26:40] INFO: Finished. +214: 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestXVal.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import CrossValidate, randomtest -214: .[03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: ..s +222: ................................... 222: ---------------------------------------------------------------------- -222: Ran 3 tests in 0.087s +222: Ran 35 tests in 1.110s 222: -222: OK (skipped=1) -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +222: OK +214: .[12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: .... 216: ---------------------------------------------------------------------- -216: Ran 4 tests in 0.284s +216: Ran 4 tests in 1.523s 216: 216: OK +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +222: .... +222: ---------------------------------------------------------------------- +222: Ran 4 tests in 0.059s +222: +222: OK +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:43] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:44] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import ID3 216: ...... 216: ---------------------------------------------------------------------- -216: Ran 6 tests in 0.011s +216: Ran 6 tests in 0.055s 216: 216: OK +222: . +222: ---------------------------------------------------------------------- +222: Ran 1 test in 0.024s +222: +222: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree 216: .. 216: ---------------------------------------------------------------------- -216: Ran 2 tests in 0.073s +216: Ran 2 tests in 0.399s 216: 216: OK +214: .[12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:45] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +222: ....... +222: ---------------------------------------------------------------------- +222: Ran 7 tests in 0.113s +222: +222: OK +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:46] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestQuantTree.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import BuildQuantTree 216: .......... 216: ---------------------------------------------------------------------- -216: Ran 10 tests in 0.007s +216: Ran 10 tests in 0.040s 216: 216: OK +222: ... +222: ---------------------------------------------------------------------- +222: Ran 3 tests in 0.087s +222: +222: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestSigTree.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble 216: ..... 216: ---------------------------------------------------------------------- -216: Ran 5 tests in 0.041s +216: Ran 5 tests in 0.237s 216: 216: OK -222: ................................... -222: ---------------------------------------------------------------------- -222: Ran 35 tests in 1.056s -222: -222: OK +214: .[12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: .. 216: ---------------------------------------------------------------------- 216: Ran 2 tests in 0.002s 216: 216: OK -222: .... -222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.011s -222: -222: OK +156: Timed out after 71 seconds. +133: [12:26:49] UFFTYPER: Unrecognized atom type: S_6+6 (0) +133: [12:26:49] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +133: [12:26:49] UFFTYPER: Unrecognized charge state for atom: 0 216: ..... 216: ---------------------------------------------------------------------- -216: Ran 5 tests in 0.008s +216: Ran 5 tests in 0.041s 216: 216: OK +222: .ss.ss....... +222: ---------------------------------------------------------------------- +222: Ran 13 tests in 2.871s +222: +222: OK (skipped=4) 216: ... 216: ---------------------------------------------------------------------- -216: Ran 3 tests in 0.007s +216: Ran 3 tests in 0.039s 216: 216: OK -222: . -222: ---------------------------------------------------------------------- -222: Ran 1 test in 0.007s -222: -222: OK -214: ....[03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: ....... -222: ---------------------------------------------------------------------- -222: Ran 7 tests in 0.024s -222: -222: OK -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +133: =============================================================================== +133: All tests passed (448 assertions in 10 test cases) +133: +215/222 Test #133: distGeomHelpersCatch ................... Passed 104.45 sec +222: [12:26:52] Molecule does not have explicit Hs. Consider calling AddHs() +222: .[12:26:52] Molecule does not have explicit Hs. Consider calling AddHs() 216: ... 216: ---------------------------------------------------------------------- -216: Ran 3 tests in 0.202s +216: Ran 3 tests in 1.006s 216: 216: OK -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: ... -222: ---------------------------------------------------------------------- -222: Ran 3 tests in 0.031s -222: -222: OK -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: ...... 216: ---------------------------------------------------------------------- -216: Ran 6 tests in 0.193s +216: Ran 6 tests in 0.963s 216: 216: OK -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:11] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: ....[12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.Composite import Composite +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.ModelPackage import Packager, PackageUtils -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/ModelPackage/UnitTestPackage.py:72: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: model = pickle.load(modelF) -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: ....... 216: ---------------------------------------------------------------------- -216: Ran 7 tests in 0.091s +216: Ran 7 tests in 0.321s 216: 216: OK -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: .ss.ss....... -222: ---------------------------------------------------------------------- -222: Ran 13 tests in 0.602s -222: -222: OK (skipped=4) -214: [03:18:12] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:57] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/NaiveBayes/UnitTestNB.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.NaiveBayes import CrossValidate +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: .... 216: ---------------------------------------------------------------------- -216: Ran 4 tests in 0.006s +216: Ran 4 tests in 0.018s 216: 216: OK -222: [03:18:12] Molecule does not have explicit Hs. Consider calling AddHs() -222: .[03:18:12] Molecule does not have explicit Hs. Consider calling AddHs() +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:58] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestTrainer.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.Neural import Network, Trainers -214: .[03:18:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: .[03:18:13] INFO: Reading molecules and constructing molecular database. -214: -214: [03:18:13] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -214: -214: [03:18:13] INFO: Processing 10 molecules -214: -214: [03:18:13] INFO: Generating fingerprints and descriptors: -214: -214: [03:18:13] INFO: Finished. -214: +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:26:59] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: .[12:27:03] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 216: ..... 216: ---------------------------------------------------------------------- -216: Ran 5 tests in 1.231s +216: Ran 5 tests in 4.729s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestOther.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH -214: [03:18:14] INFO: Reading molecules and constructing molecular database. -214: -214: [03:18:14] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt -214: -214: [03:18:14] INFO: Processing 10 molecules -214: 216: .... 216: ---------------------------------------------------------------------- -216: Ran 4 tests in 0.001s +216: Ran 4 tests in 0.006s 216: 216: OK -214: [03:18:14] INFO: Generating fingerprints and descriptors: -214: -214: [03:18:14] INFO: Finished. -214: 216: .... 216: ---------------------------------------------------------------------- 216: Ran 4 tests in 0.000s 216: 216: OK +214: .[12:27:06] INFO: Reading molecules and constructing molecular database. +214: +214: [12:27:06] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: +214: [12:27:06] INFO: Processing 10 molecules +214: +214: [12:27:06] INFO: Generating fingerprints and descriptors: +214: +214: [12:27:06] INFO: Finished. +214: 216: .... 216: ---------------------------------------------------------------------- -216: Ran 4 tests in 0.003s +216: Ran 4 tests in 0.011s 216: 216: OK -215/222 Test #216: pythonTestDirML ........................ Passed 11.43 sec -214: [03:18:14] INFO: Reading molecules and constructing molecular database. +216/222 Test #216: pythonTestDirML ........................ Passed 43.14 sec +214: [12:27:08] INFO: Reading molecules and constructing molecular database. 214: -214: [03:18:14] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: [12:27:08] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 214: -214: [03:18:14] INFO: Processing 10 molecules +214: [12:27:08] INFO: Processing 10 molecules 214: -214: [03:18:14] INFO: Generating fingerprints and descriptors: +214: [12:27:08] INFO: Generating fingerprints and descriptors: 214: -214: [03:18:14] INFO: Finished. +214: [12:27:08] INFO: Finished. 214: -169: ............. -169: ---------------------------------------------------------------------- -169: Ran 19 tests in 22.964s -169: -169: OK -169: Testing atom rings -169: testing bond rings -169: searching atom rings -169: searching bond rings -169: done -216/222 Test #169: pySubstructLibrary ..................... Passed 23.35 sec -214: [03:18:15] INFO: Reading molecules and constructing molecular database. +214: [12:27:11] INFO: Reading molecules and constructing molecular database. +214: +214: [12:27:11] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: +214: [12:27:11] INFO: Processing 10 molecules 214: -214: [03:18:15] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: [12:27:11] INFO: Generating fingerprints and descriptors: 214: -214: [03:18:15] INFO: Generating fingerprints and descriptors: +214: [12:27:11] INFO: Finished. 214: -214: [03:18:15] INFO: Finished. +214: [12:27:13] INFO: Reading molecules and constructing molecular database. 214: -214: [03:18:16] INFO: Reading molecules and constructing molecular database. +214: [12:27:13] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 214: -214: [03:18:16] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: [12:27:13] INFO: Generating fingerprints and descriptors: 214: -214: [03:18:16] INFO: Generating fingerprints and descriptors: +214: [12:27:13] INFO: Finished. 214: -214: [03:18:16] INFO: Finished. +214: [12:27:16] INFO: Reading molecules and constructing molecular database. 214: -214: .[03:18:16] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. +214: [12:27:16] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 214: -214: [03:18:16] INFO: Reading molecules and constructing molecular database. +214: [12:27:16] INFO: Generating fingerprints and descriptors: 214: -214: [03:18:16] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: [12:27:16] INFO: Finished. 214: -214: [03:18:16] INFO: Processing 163 molecules +214: .[12:27:18] INFO: Guessing that mol format is 'sdf'. Use --molFormat argument if this is wrong. 214: -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] INFO: done 100 +214: [12:27:18] INFO: Reading molecules and constructing molecular database. 214: -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:16] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] INFO: Generating fingerprints and descriptors: +214: [12:27:18] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 214: -214: [03:18:17] INFO: Finished. +214: [12:27:18] INFO: Processing 163 molecules 214: -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: [03:18:17] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -214: .[03:18:18] INFO: Reading molecules and constructing molecular database. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] INFO: done 100 214: -214: [03:18:18] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:18] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:19] INFO: Generating fingerprints and descriptors: 214: -214: [03:18:18] INFO: Processing 10 molecules +214: [12:27:19] INFO: Finished. 214: -214: [03:18:18] INFO: Generating fingerprints and descriptors: +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: [12:27:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +214: .[12:27:22] INFO: Reading molecules and constructing molecular database. 214: -214: [03:18:18] INFO: Finished. +214: [12:27:22] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt 214: -214: [03:18:19] INFO: Reading molecules and constructing molecular database. +214: [12:27:22] INFO: Processing 10 molecules 214: -214: [03:18:19] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: [12:27:22] INFO: Generating fingerprints and descriptors: 214: -214: [03:18:19] INFO: Processing 10 molecules +214: [12:27:22] INFO: Finished. 214: -214: [03:18:19] INFO: Generating fingerprints and descriptors: +214: [12:27:23] INFO: Reading molecules and constructing molecular database. 214: -214: [03:18:19] INFO: Finished. +214: [12:27:23] INFO: Generating molecular database in file testData/bzr/Compounds.sqlt +214: +214: [12:27:23] INFO: Processing 10 molecules +214: +214: [12:27:23] INFO: Generating fingerprints and descriptors: +214: +214: [12:27:23] INFO: Finished. 214: 214: . 214: ---------------------------------------------------------------------- -214: Ran 12 tests in 15.827s +214: Ran 12 tests in 60.395s 214: 214: OK -217/222 Test #214: pythonTestDbCLI ........................ Passed 16.16 sec -132: [03:18:20] done +217/222 Test #214: pythonTestDbCLI ........................ Passed 61.20 sec 157: =============================================================================== 157: All tests passed (93 assertions in 5 test cases) 157: -218/222 Test #157: testRascalCluster ...................... Passed 38.55 sec +218/222 Test #157: testRascalCluster ...................... Passed 118.38 sec +132: [12:27:36] done 132: CNC[C@H]1CC[C@H](C[NH3+])CC1 132: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 132: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 @@ -26470,10 +26501,6 @@ 132: CO[C@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 132: CO[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 132: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O -5: [03:18:24] Finished: testMultipleTimes() -5: [03:18:24] -5: ----------------------------------------- -219/222 Test #5: testConcurrentQueue .................... Passed 56.12 sec 132: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 132: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O 132: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 @@ -26483,19 +26510,19 @@ 132: O=C(O)[C@@H]1C[C@H]2C[C@@H](CCc3nn[nH]n3)CC[C@H]2CN1 132: COc1ccc2c(c1)OC[C@@H](N1CCC(O)(c3ccc(F)cc3)CC1)[C@H]2O 132: Oc1ccc2c(c1)OC[C@@H](N1CCC(Cc3ccccc3)CC1)[C@H]2O -132: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O -132: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 156: =============================================================================== 156: All tests passed (2552 assertions in 23 test cases) 156: -220/222 Test #156: testRascalMCES ......................... Passed 48.77 sec +219/222 Test #156: testRascalMCES ......................... Passed 156.72 sec +132: Oc1ccc2c(c1)OC[C@H](N1CCC(O)(c3ccccc3)CC1)[C@@H]2O +132: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 132: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 132: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 -222: ....................[03:18:31] WARNING: More than one matching pattern found - picking one +222: ....................[12:28:10] WARNING: More than one matching pattern found - picking one 222: -222: [03:18:31] WARNING: More than one matching pattern found - picking one +222: [12:28:10] WARNING: More than one matching pattern found - picking one 222: -222: .[03:18:31] WARNING: More than one matching pattern found - picking one +222: .[12:28:10] WARNING: More than one matching pattern found - picking one 222: 132: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 132: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 @@ -26504,27 +26531,27 @@ 132: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 222: ... 222: ---------------------------------------------------------------------- -222: Ran 25 tests in 20.411s +222: Ran 25 tests in 83.227s 222: 222: OK -222: {'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'} -222: {'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'} +222: {'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'} +222: {'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'} 222: {'F[C@@H](Cl)[C@@H](F)Cl', 'F[C@H](Cl)[C@H](F)Cl', 'F[C@H](Cl)[C@@H](F)Cl'} 222: !!!! ['C[C@H]([C@H](C)Br)[C@@H](C)F', 'C[C@@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)Br)[C@@H](C)F', 'C[C@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)F)[C@H](C)Br', 'C[C@@H]([C@H](C)F)[C@@H](C)Br', 'C[C@H]([C@H](C)F)[C@H](C)Br', 'C[C@H]([C@H](C)F)[C@@H](C)Br'] 222: ........ 222: ---------------------------------------------------------------------- -222: Ran 8 tests in 0.064s +222: Ran 8 tests in 0.141s 222: 222: OK -222: .[03:18:33] Molecule does not have explicit Hs. Consider calling AddHs() +222: .[12:28:16] Molecule does not have explicit Hs. Consider calling AddHs() 132: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 132: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -132: [03:18:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [03:18:34] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: F....[03:18:35] WARNING: not removing hydrogen atom without neighbors -222: [03:18:35] WARNING: not removing hydrogen atom without neighbors -222: [03:18:35] WARNING: not removing hydrogen atom without neighbors -222: ....[03:18:35] WARNING: not removing hydrogen atom without neighbors +132: [12:28:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [12:28:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +222: F....[12:28:23] WARNING: not removing hydrogen atom without neighbors +222: [12:28:23] WARNING: not removing hydrogen atom without neighbors +222: [12:28:23] WARNING: not removing hydrogen atom without neighbors +222: ....[12:28:23] WARNING: not removing hydrogen atom without neighbors 222: ...... 222: ====================================================================== 222: FAIL: testGet3DMolDescriptors (__main__.TestCase.testGet3DMolDescriptors) @@ -26535,23 +26562,23 @@ 222: AssertionError: 20.954531335493083 != 20.954531335493417 222: 222: ---------------------------------------------------------------------- -222: Ran 16 tests in 2.041s +222: Ran 16 tests in 6.462s 222: 222: FAILED (failures=1) 222: .... 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.880s +222: Ran 4 tests in 2.245s 222: 222: OK 222: ...... 222: ---------------------------------------------------------------------- -222: Ran 6 tests in 0.180s +222: Ran 6 tests in 0.667s 222: 222: OK 222: ......./build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit/Chem/PandasPatcher.py:132: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead. 222: for col in df_subset.columns[df_subset.applymap(MolFormatter.is_mol).any()] -132: [03:18:39] Molecule does not have explicit Hs. Consider calling AddHs() -221/222 Test #132: testDistGeomHelpers .................... Passed 63.54 sec +132: [12:28:33] Molecule does not have explicit Hs. Consider calling AddHs() +220/222 Test #132: testDistGeomHelpers .................... Passed 205.69 sec 222: ./build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit/Chem/PandasPatcher.py:132: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead. 222: for col in df_subset.columns[df_subset.applymap(MolFormatter.is_mol).any()] 222: ...../build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit/Chem/PandasPatcher.py:132: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead. @@ -26560,293 +26587,293 @@ 222: for col in df_subset.columns[df_subset.applymap(MolFormatter.is_mol).any()] 222: ..s..s......... 222: ---------------------------------------------------------------------- -222: Ran 28 tests in 1.616s +222: Ran 28 tests in 5.192s 222: 222: OK (skipped=2) -222: ..............[03:18:45] WARNING: More than one matching pattern found - picking one +222: ..............[12:28:50] WARNING: More than one matching pattern found - picking one 222: -222: [03:18:45] WARNING: More than one matching pattern found - picking one +222: [12:28:50] WARNING: More than one matching pattern found - picking one 222: -222: ..[03:18:45] Molecule does not have explicit Hs. Consider calling AddHs() -222: [03:18:45] Molecule does not have explicit Hs. Consider calling AddHs() -222: [03:18:45] Molecule does not have explicit Hs. Consider calling AddHs() -222: [03:18:45] Molecule does not have explicit Hs. Consider calling AddHs() +222: ..[12:28:51] Molecule does not have explicit Hs. Consider calling AddHs() +222: [12:28:51] Molecule does not have explicit Hs. Consider calling AddHs() +222: [12:28:51] Molecule does not have explicit Hs. Consider calling AddHs() +222: [12:28:51] Molecule does not have explicit Hs. Consider calling AddHs() 222: ......... 222: ---------------------------------------------------------------------- -222: Ran 25 tests in 5.104s +222: Ran 25 tests in 14.261s 222: 222: OK 222: .. 222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.028s +222: Ran 2 tests in 0.099s 222: 222: OK 222: ..s... 222: ---------------------------------------------------------------------- -222: Ran 6 tests in 0.538s +222: Ran 6 tests in 1.455s 222: 222: OK (skipped=1) 222: .. 222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.013s +222: Ran 2 tests in 0.046s 222: 222: OK 222: .............. 222: ---------------------------------------------------------------------- -222: Ran 14 tests in 2.451s +222: Ran 14 tests in 7.287s 222: 222: OK -222: ..[03:18:55] WARNING: not removing hydrogen atom without neighbors -222: .[03:18:55] WARNING: not removing hydrogen atom without neighbors -222: .[03:18:55] WARNING: no name column found on line 1 -222: [03:18:55] WARNING: no name column found on line 2 -222: [03:18:55] WARNING: no name column found on line 3 -222: [03:18:55] WARNING: no name column found on line 4 -222: [03:18:55] WARNING: no name column found on line 5 -222: [03:18:55] WARNING: no name column found on line 6 -222: [03:18:55] WARNING: no name column found on line 7 -222: [03:18:55] WARNING: no name column found on line 8 -222: [03:18:55] WARNING: no name column found on line 9 -222: [03:18:55] WARNING: no name column found on line 10 -222: [03:18:55] WARNING: no name column found on line 11 -222: [03:18:55] WARNING: no name column found on line 12 -222: [03:18:55] WARNING: no name column found on line 13 -222: [03:18:55] WARNING: no name column found on line 14 -222: [03:18:55] WARNING: no name column found on line 15 -222: [03:18:55] WARNING: no name column found on line 16 -222: [03:18:55] WARNING: no name column found on line 17 -222: [03:18:55] WARNING: no name column found on line 18 -222: [03:18:55] WARNING: no name column found on line 19 -222: [03:18:55] WARNING: no name column found on line 20 -222: [03:18:55] WARNING: no name column found on line 21 -222: [03:18:55] WARNING: no name column found on line 22 -222: [03:18:55] WARNING: no name column found on line 23 -222: [03:18:55] WARNING: no name column found on line 24 -222: [03:18:55] WARNING: no name column found on line 25 -222: [03:18:55] WARNING: no name column found on line 26 -222: [03:18:55] WARNING: no name column found on line 27 -222: [03:18:55] WARNING: no name column found on line 28 -222: [03:18:55] WARNING: no name column found on line 29 -222: [03:18:55] WARNING: no name column found on line 30 -222: [03:18:55] WARNING: no name column found on line 31 -222: [03:18:55] WARNING: no name column found on line 32 -222: [03:18:55] WARNING: no name column found on line 33 -222: [03:18:55] WARNING: no name column found on line 34 -222: [03:18:55] WARNING: no name column found on line 35 -222: [03:18:55] WARNING: no name column found on line 36 -222: [03:18:55] WARNING: no name column found on line 37 -222: [03:18:55] WARNING: no name column found on line 38 -222: [03:18:55] WARNING: no name column found on line 39 -222: [03:18:55] WARNING: no name column found on line 40 -222: [03:18:55] WARNING: no name column found on line 41 -222: [03:18:55] WARNING: no name column found on line 42 -222: [03:18:55] WARNING: no name column found on line 43 -222: [03:18:55] WARNING: no name column found on line 44 -222: [03:18:55] WARNING: no name column found on line 45 -222: [03:18:55] WARNING: no name column found on line 46 -222: [03:18:55] WARNING: no name column found on line 47 -222: [03:18:55] WARNING: no name column found on line 48 -222: [03:18:55] WARNING: no name column found on line 49 -222: [03:18:55] WARNING: no name column found on line 50 -222: [03:18:55] WARNING: no name column found on line 51 -222: [03:18:55] WARNING: no name column found on line 52 -222: [03:18:55] WARNING: no name column found on line 53 -222: [03:18:55] WARNING: no name column found on line 54 -222: [03:18:55] WARNING: no name column found on line 55 -222: [03:18:55] WARNING: no name column found on line 56 -222: [03:18:55] WARNING: no name column found on line 57 -222: [03:18:55] WARNING: no name column found on line 58 -222: [03:18:55] WARNING: no name column found on line 59 -222: [03:18:55] WARNING: no name column found on line 60 -222: [03:18:55] WARNING: no name column found on line 61 -222: [03:18:55] WARNING: no name column found on line 62 -222: [03:18:55] WARNING: no name column found on line 63 -222: [03:18:55] WARNING: no name column found on line 64 -222: [03:18:55] WARNING: no name column found on line 65 -222: [03:18:55] WARNING: no name column found on line 66 -222: [03:18:55] WARNING: no name column found on line 67 -222: [03:18:55] WARNING: no name column found on line 68 -222: [03:18:55] WARNING: no name column found on line 69 -222: [03:18:55] WARNING: no name column found on line 70 -222: [03:18:55] WARNING: no name column found on line 71 -222: [03:18:55] WARNING: no name column found on line 72 -222: [03:18:55] WARNING: no name column found on line 73 -222: [03:18:55] WARNING: no name column found on line 74 -222: [03:18:55] WARNING: no name column found on line 75 -222: [03:18:55] WARNING: no name column found on line 76 -222: [03:18:55] WARNING: no name column found on line 77 -222: [03:18:55] WARNING: no name column found on line 78 -222: [03:18:55] WARNING: no name column found on line 79 -222: [03:18:55] WARNING: no name column found on line 80 -222: [03:18:55] WARNING: no name column found on line 81 -222: [03:18:55] WARNING: no name column found on line 82 -222: [03:18:55] WARNING: no name column found on line 83 -222: [03:18:55] WARNING: no name column found on line 84 -222: [03:18:55] WARNING: no name column found on line 85 -222: [03:18:55] WARNING: no name column found on line 86 -222: [03:18:55] WARNING: no name column found on line 87 -222: [03:18:55] WARNING: no name column found on line 88 -222: [03:18:55] WARNING: no name column found on line 89 -222: [03:18:55] WARNING: no name column found on line 90 -222: [03:18:55] WARNING: no name column found on line 91 -222: [03:18:55] WARNING: no name column found on line 92 -222: [03:18:55] WARNING: no name column found on line 93 -222: [03:18:55] WARNING: no name column found on line 94 -222: [03:18:55] WARNING: no name column found on line 95 -222: [03:18:55] WARNING: no name column found on line 96 -222: [03:18:55] WARNING: no name column found on line 97 -222: [03:18:55] WARNING: no name column found on line 98 -222: [03:18:55] WARNING: no name column found on line 99 -222: [03:18:55] WARNING: no name column found on line 100 -222: [03:18:55] WARNING: no name column found on line 101 -222: [03:18:55] WARNING: no name column found on line 102 -222: [03:18:55] WARNING: no name column found on line 103 -222: [03:18:55] WARNING: no name column found on line 104 -222: [03:18:55] WARNING: no name column found on line 105 -222: [03:18:55] WARNING: no name column found on line 106 -222: [03:18:55] WARNING: no name column found on line 107 -222: [03:18:55] WARNING: no name column found on line 108 -222: [03:18:55] WARNING: no name column found on line 109 -222: [03:18:55] WARNING: no name column found on line 110 -222: [03:18:55] WARNING: no name column found on line 111 -222: [03:18:55] WARNING: no name column found on line 112 -222: [03:18:55] WARNING: no name column found on line 113 -222: [03:18:55] WARNING: no name column found on line 114 -222: [03:18:55] WARNING: no name column found on line 115 -222: [03:18:55] WARNING: no name column found on line 116 -222: [03:18:55] WARNING: no name column found on line 117 -222: [03:18:55] WARNING: no name column found on line 118 -222: [03:18:55] WARNING: no name column found on line 119 -222: [03:18:55] WARNING: no name column found on line 120 -222: [03:18:55] WARNING: no name column found on line 121 -222: [03:18:55] WARNING: no name column found on line 122 -222: [03:18:55] WARNING: no name column found on line 123 -222: [03:18:55] WARNING: no name column found on line 124 -222: [03:18:55] WARNING: no name column found on line 125 -222: [03:18:55] WARNING: no name column found on line 126 -222: [03:18:55] WARNING: no name column found on line 127 -222: [03:18:55] WARNING: no name column found on line 128 -222: [03:18:55] WARNING: no name column found on line 129 -222: [03:18:55] WARNING: no name column found on line 130 -222: [03:18:55] WARNING: no name column found on line 131 -222: [03:18:55] WARNING: no name column found on line 132 -222: [03:18:55] WARNING: no name column found on line 133 -222: [03:18:55] WARNING: no name column found on line 134 -222: [03:18:55] WARNING: no name column found on line 135 -222: [03:18:55] WARNING: no name column found on line 136 -222: [03:18:55] WARNING: no name column found on line 137 -222: [03:18:55] WARNING: no name column found on line 138 -222: [03:18:55] WARNING: no name column found on line 139 -222: [03:18:55] WARNING: no name column found on line 140 -222: [03:18:55] WARNING: no name column found on line 141 -222: [03:18:55] WARNING: no name column found on line 142 -222: [03:18:55] WARNING: no name column found on line 143 -222: [03:18:55] WARNING: no name column found on line 144 -222: [03:18:55] WARNING: no name column found on line 145 -222: [03:18:55] WARNING: no name column found on line 146 -222: [03:18:55] WARNING: no name column found on line 147 -222: [03:18:55] WARNING: no name column found on line 148 -222: [03:18:55] WARNING: no name column found on line 149 -222: [03:18:55] WARNING: no name column found on line 150 -222: [03:18:55] WARNING: no name column found on line 151 -222: [03:18:55] WARNING: no name column found on line 152 -222: [03:18:55] WARNING: no name column found on line 153 -222: [03:18:55] WARNING: no name column found on line 154 -222: [03:18:55] WARNING: no name column found on line 155 -222: [03:18:55] WARNING: no name column found on line 156 -222: [03:18:55] WARNING: no name column found on line 157 -222: [03:18:55] WARNING: no name column found on line 158 -222: [03:18:55] WARNING: no name column found on line 159 -222: [03:18:55] WARNING: no name column found on line 160 -222: [03:18:55] WARNING: no name column found on line 161 -222: [03:18:55] WARNING: no name column found on line 162 -222: [03:18:55] WARNING: no name column found on line 163 -222: [03:18:55] WARNING: no name column found on line 164 -222: [03:18:55] WARNING: no name column found on line 165 -222: [03:18:55] WARNING: no name column found on line 166 -222: [03:18:55] WARNING: no name column found on line 167 -222: [03:18:55] WARNING: no name column found on line 168 -222: [03:18:55] WARNING: no name column found on line 169 -222: [03:18:55] WARNING: no name column found on line 170 -222: [03:18:55] WARNING: no name column found on line 171 -222: [03:18:55] WARNING: no name column found on line 172 -222: [03:18:55] WARNING: no name column found on line 173 -222: [03:18:55] WARNING: no name column found on line 174 -222: [03:18:55] WARNING: no name column found on line 175 -222: [03:18:55] WARNING: no name column found on line 176 -222: [03:18:55] WARNING: no name column found on line 177 -222: [03:18:55] WARNING: no name column found on line 178 -222: [03:18:55] WARNING: no name column found on line 179 -222: [03:18:55] WARNING: no name column found on line 180 -222: [03:18:55] WARNING: no name column found on line 181 -222: [03:18:55] WARNING: no name column found on line 182 -222: [03:18:55] WARNING: no name column found on line 183 -222: [03:18:55] WARNING: no name column found on line 184 -222: [03:18:55] WARNING: no name column found on line 185 -222: [03:18:55] WARNING: no name column found on line 186 -222: [03:18:55] WARNING: no name column found on line 187 -222: [03:18:55] WARNING: no name column found on line 188 -222: [03:18:55] WARNING: no name column found on line 189 -222: [03:18:55] WARNING: no name column found on line 190 -222: [03:18:55] WARNING: no name column found on line 191 -222: [03:18:55] WARNING: no name column found on line 192 -222: [03:18:55] WARNING: no name column found on line 193 -222: [03:18:55] WARNING: no name column found on line 194 -222: [03:18:55] WARNING: no name column found on line 195 -222: [03:18:55] WARNING: no name column found on line 196 -222: [03:18:55] WARNING: no name column found on line 197 -222: [03:18:55] WARNING: no name column found on line 198 -222: [03:18:55] WARNING: no name column found on line 199 -222: [03:18:55] WARNING: no name column found on line 200 -222: [03:18:55] WARNING: no name column found on line 201 -222: [03:18:55] WARNING: no name column found on line 202 -222: [03:18:55] WARNING: no name column found on line 203 -222: [03:18:55] WARNING: no name column found on line 204 -222: [03:18:55] WARNING: no name column found on line 205 -222: [03:18:55] WARNING: no name column found on line 206 -222: [03:18:55] WARNING: no name column found on line 207 -222: [03:18:55] WARNING: no name column found on line 208 -222: [03:18:55] WARNING: no name column found on line 209 -222: [03:18:55] WARNING: no name column found on line 210 -222: [03:18:55] WARNING: no name column found on line 211 -222: [03:18:55] WARNING: no name column found on line 212 -222: [03:18:55] WARNING: no name column found on line 213 -222: [03:18:55] WARNING: no name column found on line 214 -222: [03:18:55] WARNING: no name column found on line 215 -222: [03:18:55] WARNING: no name column found on line 216 +222: ..[12:29:16] WARNING: not removing hydrogen atom without neighbors +222: .[12:29:16] WARNING: not removing hydrogen atom without neighbors +222: .[12:29:16] WARNING: no name column found on line 1 +222: [12:29:16] WARNING: no name column found on line 2 +222: [12:29:16] WARNING: no name column found on line 3 +222: [12:29:16] WARNING: no name column found on line 4 +222: [12:29:16] WARNING: no name column found on line 5 +222: [12:29:16] WARNING: no name column found on line 6 +222: [12:29:16] WARNING: no name column found on line 7 +222: [12:29:16] WARNING: no name column found on line 8 +222: [12:29:16] WARNING: no name column found on line 9 +222: [12:29:16] WARNING: no name column found on line 10 +222: [12:29:16] WARNING: no name column found on line 11 +222: [12:29:16] WARNING: no name column found on line 12 +222: [12:29:16] WARNING: no name column found on line 13 +222: [12:29:16] WARNING: no name column found on line 14 +222: [12:29:16] WARNING: no name column found on line 15 +222: [12:29:16] WARNING: no name column found on line 16 +222: [12:29:16] WARNING: no name column found on line 17 +222: [12:29:16] WARNING: no name column found on line 18 +222: [12:29:16] WARNING: no name column found on line 19 +222: [12:29:16] WARNING: no name column found on line 20 +222: [12:29:16] WARNING: no name column found on line 21 +222: [12:29:16] WARNING: no name column found on line 22 +222: [12:29:16] WARNING: no name column found on line 23 +222: [12:29:16] WARNING: no name column found on line 24 +222: [12:29:16] WARNING: no name column found on line 25 +222: [12:29:16] WARNING: no name column found on line 26 +222: [12:29:16] WARNING: no name column found on line 27 +222: [12:29:16] WARNING: no name column found on line 28 +222: [12:29:16] WARNING: no name column found on line 29 +222: [12:29:16] WARNING: no name column found on line 30 +222: [12:29:16] WARNING: no name column found on line 31 +222: [12:29:16] WARNING: no name column found on line 32 +222: [12:29:16] WARNING: no name column found on line 33 +222: [12:29:16] WARNING: no name column found on line 34 +222: [12:29:16] WARNING: no name column found on line 35 +222: [12:29:16] WARNING: no name column found on line 36 +222: [12:29:16] WARNING: no name column found on line 37 +222: [12:29:16] WARNING: no name column found on line 38 +222: [12:29:16] WARNING: no name column found on line 39 +222: [12:29:16] WARNING: no name column found on line 40 +222: [12:29:16] WARNING: no name column found on line 41 +222: [12:29:16] WARNING: no name column found on line 42 +222: [12:29:16] WARNING: no name column found on line 43 +222: [12:29:16] WARNING: no name column found on line 44 +222: [12:29:16] WARNING: no name column found on line 45 +222: [12:29:16] WARNING: no name column found on line 46 +222: [12:29:16] WARNING: no name column found on line 47 +222: [12:29:16] WARNING: no name column found on line 48 +222: [12:29:16] WARNING: no name column found on line 49 +222: [12:29:16] WARNING: no name column found on line 50 +222: [12:29:16] WARNING: no name column found on line 51 +222: [12:29:16] WARNING: no name column found on line 52 +222: [12:29:16] WARNING: no name column found on line 53 +222: [12:29:16] WARNING: no name column found on line 54 +222: [12:29:16] WARNING: no name column found on line 55 +222: [12:29:16] WARNING: no name column found on line 56 +222: [12:29:16] WARNING: no name column found on line 57 +222: [12:29:16] WARNING: no name column found on line 58 +222: [12:29:16] WARNING: no name column found on line 59 +222: [12:29:16] WARNING: no name column found on line 60 +222: [12:29:16] WARNING: no name column found on line 61 +222: [12:29:16] WARNING: no name column found on line 62 +222: [12:29:16] WARNING: no name column found on line 63 +222: [12:29:16] WARNING: no name column found on line 64 +222: [12:29:16] WARNING: no name column found on line 65 +222: [12:29:16] WARNING: no name column found on line 66 +222: [12:29:16] WARNING: no name column found on line 67 +222: [12:29:16] WARNING: no name column found on line 68 +222: [12:29:16] WARNING: no name column found on line 69 +222: [12:29:16] WARNING: no name column found on line 70 +222: [12:29:16] WARNING: no name column found on line 71 +222: [12:29:16] WARNING: no name column found on line 72 +222: [12:29:16] WARNING: no name column found on line 73 +222: [12:29:16] WARNING: no name column found on line 74 +222: [12:29:16] WARNING: no name column found on line 75 +222: [12:29:16] WARNING: no name column found on line 76 +222: [12:29:16] WARNING: no name column found on line 77 +222: [12:29:16] WARNING: no name column found on line 78 +222: [12:29:16] WARNING: no name column found on line 79 +222: [12:29:16] WARNING: no name column found on line 80 +222: [12:29:16] WARNING: no name column found on line 81 +222: [12:29:16] WARNING: no name column found on line 82 +222: [12:29:16] WARNING: no name column found on line 83 +222: [12:29:16] WARNING: no name column found on line 84 +222: [12:29:16] WARNING: no name column found on line 85 +222: [12:29:16] WARNING: no name column found on line 86 +222: [12:29:16] WARNING: no name column found on line 87 +222: [12:29:16] WARNING: no name column found on line 88 +222: [12:29:16] WARNING: no name column found on line 89 +222: [12:29:16] WARNING: no name column found on line 90 +222: [12:29:16] WARNING: no name column found on line 91 +222: [12:29:16] WARNING: no name column found on line 92 +222: [12:29:16] WARNING: no name column found on line 93 +222: [12:29:16] WARNING: no name column found on line 94 +222: [12:29:16] WARNING: no name column found on line 95 +222: [12:29:16] WARNING: no name column found on line 96 +222: [12:29:16] WARNING: no name column found on line 97 +222: [12:29:16] WARNING: no name column found on line 98 +222: [12:29:16] WARNING: no name column found on line 99 +222: [12:29:16] WARNING: no name column found on line 100 +222: [12:29:16] WARNING: no name column found on line 101 +222: [12:29:16] WARNING: no name column found on line 102 +222: [12:29:16] WARNING: no name column found on line 103 +222: [12:29:16] WARNING: no name column found on line 104 +222: [12:29:16] WARNING: no name column found on line 105 +222: [12:29:16] WARNING: no name column found on line 106 +222: [12:29:16] WARNING: no name column found on line 107 +222: [12:29:16] WARNING: no name column found on line 108 +222: [12:29:16] WARNING: no name column found on line 109 +222: [12:29:16] WARNING: no name column found on line 110 +222: [12:29:16] WARNING: no name column found on line 111 +222: [12:29:16] WARNING: no name column found on line 112 +222: [12:29:16] WARNING: no name column found on line 113 +222: [12:29:16] WARNING: no name column found on line 114 +222: [12:29:16] WARNING: no name column found on line 115 +222: [12:29:16] WARNING: no name column found on line 116 +222: [12:29:16] WARNING: no name column found on line 117 +222: [12:29:16] WARNING: no name column found on line 118 +222: [12:29:16] WARNING: no name column found on line 119 +222: [12:29:16] WARNING: no name column found on line 120 +222: [12:29:16] WARNING: no name column found on line 121 +222: [12:29:16] WARNING: no name column found on line 122 +222: [12:29:16] WARNING: no name column found on line 123 +222: [12:29:16] WARNING: no name column found on line 124 +222: [12:29:16] WARNING: no name column found on line 125 +222: [12:29:16] WARNING: no name column found on line 126 +222: [12:29:16] WARNING: no name column found on line 127 +222: [12:29:16] WARNING: no name column found on line 128 +222: [12:29:16] WARNING: no name column found on line 129 +222: [12:29:16] WARNING: no name column found on line 130 +222: [12:29:16] WARNING: no name column found on line 131 +222: [12:29:16] WARNING: no name column found on line 132 +222: [12:29:16] WARNING: no name column found on line 133 +222: [12:29:16] WARNING: no name column found on line 134 +222: [12:29:16] WARNING: no name column found on line 135 +222: [12:29:16] WARNING: no name column found on line 136 +222: [12:29:16] WARNING: no name column found on line 137 +222: [12:29:16] WARNING: no name column found on line 138 +222: [12:29:16] WARNING: no name column found on line 139 +222: [12:29:16] WARNING: no name column found on line 140 +222: [12:29:16] WARNING: no name column found on line 141 +222: [12:29:16] WARNING: no name column found on line 142 +222: [12:29:16] WARNING: no name column found on line 143 +222: [12:29:16] WARNING: no name column found on line 144 +222: [12:29:16] WARNING: no name column found on line 145 +222: [12:29:16] WARNING: no name column found on line 146 +222: [12:29:16] WARNING: no name column found on line 147 +222: [12:29:16] WARNING: no name column found on line 148 +222: [12:29:16] WARNING: no name column found on line 149 +222: [12:29:16] WARNING: no name column found on line 150 +222: [12:29:16] WARNING: no name column found on line 151 +222: [12:29:16] WARNING: no name column found on line 152 +222: [12:29:16] WARNING: no name column found on line 153 +222: [12:29:16] WARNING: no name column found on line 154 +222: [12:29:16] WARNING: no name column found on line 155 +222: [12:29:16] WARNING: no name column found on line 156 +222: [12:29:16] WARNING: no name column found on line 157 +222: [12:29:16] WARNING: no name column found on line 158 +222: [12:29:16] WARNING: no name column found on line 159 +222: [12:29:16] WARNING: no name column found on line 160 +222: [12:29:16] WARNING: no name column found on line 161 +222: [12:29:16] WARNING: no name column found on line 162 +222: [12:29:16] WARNING: no name column found on line 163 +222: [12:29:16] WARNING: no name column found on line 164 +222: [12:29:16] WARNING: no name column found on line 165 +222: [12:29:16] WARNING: no name column found on line 166 +222: [12:29:16] WARNING: no name column found on line 167 +222: [12:29:16] WARNING: no name column found on line 168 +222: [12:29:16] WARNING: no name column found on line 169 +222: [12:29:16] WARNING: no name column found on line 170 +222: [12:29:16] WARNING: no name column found on line 171 +222: [12:29:16] WARNING: no name column found on line 172 +222: [12:29:16] WARNING: no name column found on line 173 +222: [12:29:16] WARNING: no name column found on line 174 +222: [12:29:16] WARNING: no name column found on line 175 +222: [12:29:16] WARNING: no name column found on line 176 +222: [12:29:16] WARNING: no name column found on line 177 +222: [12:29:16] WARNING: no name column found on line 178 +222: [12:29:16] WARNING: no name column found on line 179 +222: [12:29:16] WARNING: no name column found on line 180 +222: [12:29:16] WARNING: no name column found on line 181 +222: [12:29:16] WARNING: no name column found on line 182 +222: [12:29:16] WARNING: no name column found on line 183 +222: [12:29:16] WARNING: no name column found on line 184 +222: [12:29:16] WARNING: no name column found on line 185 +222: [12:29:16] WARNING: no name column found on line 186 +222: [12:29:16] WARNING: no name column found on line 187 +222: [12:29:16] WARNING: no name column found on line 188 +222: [12:29:16] WARNING: no name column found on line 189 +222: [12:29:16] WARNING: no name column found on line 190 +222: [12:29:16] WARNING: no name column found on line 191 +222: [12:29:16] WARNING: no name column found on line 192 +222: [12:29:16] WARNING: no name column found on line 193 +222: [12:29:16] WARNING: no name column found on line 194 +222: [12:29:16] WARNING: no name column found on line 195 +222: [12:29:16] WARNING: no name column found on line 196 +222: [12:29:16] WARNING: no name column found on line 197 +222: [12:29:16] WARNING: no name column found on line 198 +222: [12:29:16] WARNING: no name column found on line 199 +222: [12:29:16] WARNING: no name column found on line 200 +222: [12:29:16] WARNING: no name column found on line 201 +222: [12:29:16] WARNING: no name column found on line 202 +222: [12:29:16] WARNING: no name column found on line 203 +222: [12:29:16] WARNING: no name column found on line 204 +222: [12:29:16] WARNING: no name column found on line 205 +222: [12:29:16] WARNING: no name column found on line 206 +222: [12:29:16] WARNING: no name column found on line 207 +222: [12:29:16] WARNING: no name column found on line 208 +222: [12:29:16] WARNING: no name column found on line 209 +222: [12:29:16] WARNING: no name column found on line 210 +222: [12:29:16] WARNING: no name column found on line 211 +222: [12:29:16] WARNING: no name column found on line 212 +222: [12:29:16] WARNING: no name column found on line 213 +222: [12:29:16] WARNING: no name column found on line 214 +222: [12:29:16] WARNING: no name column found on line 215 +222: [12:29:16] WARNING: no name column found on line 216 222: ...... 222: ---------------------------------------------------------------------- -222: Ran 10 tests in 0.083s +222: Ran 10 tests in 0.174s 222: 222: OK 222: .................. 222: ---------------------------------------------------------------------- -222: Ran 18 tests in 0.526s +222: Ran 18 tests in 1.335s 222: 222: OK 222: ... 222: ---------------------------------------------------------------------- -222: Ran 3 tests in 0.057s +222: Ran 3 tests in 0.177s 222: 222: OK 222: ........ 222: ---------------------------------------------------------------------- -222: Ran 8 tests in 0.020s +222: Ran 8 tests in 0.062s 222: 222: OK 222: .. 222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.014s +222: Ran 2 tests in 0.056s 222: 222: OK 222: .. 222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.010s +222: Ran 2 tests in 0.039s 222: 222: OK 222: . 222: ---------------------------------------------------------------------- -222: Ran 1 test in 0.047s +222: Ran 1 test in 0.164s 222: 222: OK 222: ........ @@ -26856,7 +26883,7 @@ 222: OK 222: ... 222: ---------------------------------------------------------------------- -222: Ran 3 tests in 0.003s +222: Ran 3 tests in 0.012s 222: 222: OK 222: ... @@ -26866,27 +26893,27 @@ 222: OK 222: .... 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.002s +222: Ran 4 tests in 0.015s 222: 222: OK 222: ....... 222: ---------------------------------------------------------------------- -222: Ran 7 tests in 0.009s +222: Ran 7 tests in 0.025s 222: 222: OK 222: .... 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.011s +222: Ran 4 tests in 0.048s 222: 222: OK 222: .... 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 1.509s +222: Ran 4 tests in 6.230s 222: 222: OK 222: .......... 222: ---------------------------------------------------------------------- -222: Ran 10 tests in 0.031s +222: Ran 10 tests in 0.123s 222: 222: OK 222: . @@ -26896,23 +26923,23 @@ 222: OK 222: .......... 222: ---------------------------------------------------------------------- -222: Ran 10 tests in 0.004s +222: Ran 10 tests in 0.014s 222: 222: OK 222: ..... 222: ---------------------------------------------------------------------- -222: Ran 5 tests in 0.046s +222: Ran 5 tests in 0.090s 222: 222: OK -222: .........[03:19:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: [03:19:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: [03:19:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: [03:19:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -222: .......[03:19:08] Molecule does not have explicit Hs. Consider calling AddHs() -222: [03:19:08] Molecule does not have explicit Hs. Consider calling AddHs() +222: .........[12:29:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +222: [12:29:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +222: [12:29:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +222: [12:29:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +222: .......[12:29:56] Molecule does not have explicit Hs. Consider calling AddHs() +222: [12:29:56] Molecule does not have explicit Hs. Consider calling AddHs() 222: ..... 222: ---------------------------------------------------------------------- -222: Ran 21 tests in 3.224s +222: Ran 21 tests in 12.096s 222: 222: OK 222: mol_197 @@ -26926,7 +26953,7 @@ 222: Ran 1 test in 0.000s 222: 222: OK -222: ...[03:19:08] +222: ...[12:29:58] 222: 222: **** 222: Pre-condition Violation @@ -26937,63 +26964,63 @@ 222: 222: . 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.013s +222: Ran 4 tests in 0.038s 222: 222: OK 222: .. 222: ---------------------------------------------------------------------- -222: Ran 2 tests in 4.193s +222: Ran 2 tests in 12.761s 222: 222: OK 222: .. 222: ---------------------------------------------------------------------- -222: Ran 2 tests in 0.054s +222: Ran 2 tests in 0.120s 222: 222: OK 222: ... 222: ---------------------------------------------------------------------- -222: Ran 3 tests in 0.008s +222: Ran 3 tests in 0.012s 222: 222: OK 222: .... 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.013s +222: Ran 4 tests in 0.030s 222: 222: OK -222: .....[03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors -222: [03:19:15] WARNING: not removing hydrogen atom without neighbors +222: .....[12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors +222: [12:30:16] WARNING: not removing hydrogen atom without neighbors 222: ..... 222: ---------------------------------------------------------------------- -222: Ran 10 tests in 0.189s +222: Ran 10 tests in 0.710s 222: 222: OK 222: ssssss..........s/build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit/Chem/Draw/__init__.py:237: DeprecationWarning: legacy DrawingOptions not translated for new drawing code, please update manually 222: warnings.warn( 222: ..... 222: ---------------------------------------------------------------------- -222: Ran 22 tests in 2.864s +222: Ran 22 tests in 12.141s 222: 222: OK (skipped=7) 222: sss. 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.261s +222: Ran 4 tests in 0.982s 222: 222: OK (skipped=3) 222: ssss @@ -27003,49 +27030,49 @@ 222: OK (skipped=4) 222: .......... 222: ---------------------------------------------------------------------- -222: Ran 10 tests in 0.489s +222: Ran 10 tests in 2.225s 222: 222: OK -222: ...[03:19:21] SMARTS Parse Error: syntax error while parsing: boromicacid -222: [03:19:21] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -222: [03:19:21] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -222: [03:19:21] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -222: [03:19:21] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -222: [03:19:21] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -222: [03:19:21] reaction has no reactants -222: [03:19:21] reaction has no products -222: [03:19:21] initialization failed -222: [03:19:21] reaction has no reactants -222: [03:19:21] reaction has no products +222: ...[12:30:41] SMARTS Parse Error: syntax error while parsing: boromicacid +222: [12:30:41] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +222: [12:30:41] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +222: [12:30:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +222: [12:30:41] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +222: [12:30:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +222: [12:30:41] reaction has no reactants +222: [12:30:41] reaction has no products +222: [12:30:41] initialization failed +222: [12:30:41] reaction has no reactants +222: [12:30:41] reaction has no products 222: . 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.022s +222: Ran 4 tests in 0.136s 222: 222: OK 222: ['C[C@@H](F)CN', 'C[C@@H](F)CN |a:1|', 'C[C@H](F)CN |o1:1|', 'C[C@H](F)CN |&1:1|'] 222: .... 222: ---------------------------------------------------------------------- -222: Ran 4 tests in 0.007s +222: Ran 4 tests in 0.032s 222: 222: OK 222: ........................ 222: ---------------------------------------------------------------------- -222: Ran 24 tests in 0.050s +222: Ran 24 tests in 0.246s 222: 222: OK 222: !!! TEST FAILURE: python UnitTestDescriptors.py {} -222/222 Test #222: pythonTestDirChem ......................***Failed 75.94 sec +221/222 Test #222: pythonTestDirChem ......................***Failed 256.42 sec ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.060s +Ran 7 tests in 0.315s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.023s +Ran 6 tests in 0.096s OK -....[03:18:07] +....[12:26:34] **** Pre-condition Violation @@ -27056,91 +27083,91 @@ . ---------------------------------------------------------------------- -Ran 5 tests in 0.006s +Ran 5 tests in 0.034s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.006s +Ran 4 tests in 0.023s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.007s +Ran 2 tests in 0.035s OK ...................... ---------------------------------------------------------------------- -Ran 22 tests in 0.019s +Ran 22 tests in 0.083s OK .....s.................ss ---------------------------------------------------------------------- -Ran 25 tests in 0.074s +Ran 25 tests in 0.399s OK (skipped=3) ..s ---------------------------------------------------------------------- -Ran 3 tests in 0.087s +Ran 3 tests in 0.290s OK (skipped=1) ................................... ---------------------------------------------------------------------- -Ran 35 tests in 1.056s +Ran 35 tests in 1.110s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.011s +Ran 4 tests in 0.059s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.007s +Ran 1 test in 0.024s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.024s +Ran 7 tests in 0.113s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.031s +Ran 3 tests in 0.087s OK .ss.ss....... ---------------------------------------------------------------------- -Ran 13 tests in 0.602s +Ran 13 tests in 2.871s OK (skipped=4) -[03:18:12] Molecule does not have explicit Hs. Consider calling AddHs() -.[03:18:12] Molecule does not have explicit Hs. Consider calling AddHs() -....................[03:18:31] WARNING: More than one matching pattern found - picking one +[12:26:52] Molecule does not have explicit Hs. Consider calling AddHs() +.[12:26:52] Molecule does not have explicit Hs. Consider calling AddHs() +....................[12:28:10] WARNING: More than one matching pattern found - picking one -[03:18:31] WARNING: More than one matching pattern found - picking one +[12:28:10] WARNING: More than one matching pattern found - picking one -.[03:18:31] WARNING: More than one matching pattern found - picking one +.[12:28:10] WARNING: More than one matching pattern found - picking one ... ---------------------------------------------------------------------- -Ran 25 tests in 20.411s +Ran 25 tests in 83.227s 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'} +{'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@H]([C@H](C)Br)[C@@H](C)F', 'C[C@@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)Br)[C@@H](C)F', 'C[C@H]([C@@H](C)F)[C@@H](C)Br', 'C[C@@H]([C@H](C)F)[C@H](C)Br', 'C[C@@H]([C@H](C)F)[C@@H](C)Br', 'C[C@H]([C@H](C)F)[C@H](C)Br', 'C[C@H]([C@H](C)F)[C@@H](C)Br'] ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.064s +Ran 8 tests in 0.141s OK -.[03:18:33] Molecule does not have explicit Hs. Consider calling AddHs() -F....[03:18:35] WARNING: not removing hydrogen atom without neighbors -[03:18:35] WARNING: not removing hydrogen atom without neighbors -[03:18:35] WARNING: not removing hydrogen atom without neighbors -....[03:18:35] WARNING: not removing hydrogen atom without neighbors +.[12:28:16] Molecule does not have explicit Hs. Consider calling AddHs() +F....[12:28:23] WARNING: not removing hydrogen atom without neighbors +[12:28:23] WARNING: not removing hydrogen atom without neighbors +[12:28:23] WARNING: not removing hydrogen atom without neighbors +....[12:28:23] WARNING: not removing hydrogen atom without neighbors ...... ====================================================================== FAIL: testGet3DMolDescriptors (__main__.TestCase.testGet3DMolDescriptors) @@ -27151,17 +27178,17 @@ AssertionError: 20.954531335493083 != 20.954531335493417 ---------------------------------------------------------------------- -Ran 16 tests in 2.041s +Ran 16 tests in 6.462s FAILED (failures=1) .... ---------------------------------------------------------------------- -Ran 4 tests in 0.880s +Ran 4 tests in 2.245s OK ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.180s +Ran 6 tests in 0.667s OK ......./build/reproducible-path/rdkit-202309.3/obj-aarch64-linux-gnu/rdkit/Chem/PandasPatcher.py:132: FutureWarning: DataFrame.applymap has been deprecated. Use DataFrame.map instead. @@ -27174,293 +27201,293 @@ for col in df_subset.columns[df_subset.applymap(MolFormatter.is_mol).any()] ..s..s......... ---------------------------------------------------------------------- -Ran 28 tests in 1.616s +Ran 28 tests in 5.192s OK (skipped=2) -..............[03:18:45] WARNING: More than one matching pattern found - picking one +..............[12:28:50] WARNING: More than one matching pattern found - picking one -[03:18:45] WARNING: More than one matching pattern found - picking one +[12:28:50] WARNING: More than one matching pattern found - picking one -..[03:18:45] Molecule does not have explicit Hs. Consider calling AddHs() -[03:18:45] Molecule does not have explicit Hs. Consider calling AddHs() -[03:18:45] Molecule does not have explicit Hs. Consider calling AddHs() -[03:18:45] Molecule does not have explicit Hs. Consider calling AddHs() +..[12:28:51] Molecule does not have explicit Hs. Consider calling AddHs() +[12:28:51] Molecule does not have explicit Hs. Consider calling AddHs() +[12:28:51] Molecule does not have explicit Hs. Consider calling AddHs() +[12:28:51] Molecule does not have explicit Hs. Consider calling AddHs() ......... ---------------------------------------------------------------------- -Ran 25 tests in 5.104s +Ran 25 tests in 14.261s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.028s +Ran 2 tests in 0.099s OK ..s... ---------------------------------------------------------------------- -Ran 6 tests in 0.538s +Ran 6 tests in 1.455s OK (skipped=1) .. ---------------------------------------------------------------------- -Ran 2 tests in 0.013s +Ran 2 tests in 0.046s OK .............. ---------------------------------------------------------------------- -Ran 14 tests in 2.451s +Ran 14 tests in 7.287s OK -..[03:18:55] WARNING: not removing hydrogen atom without neighbors -.[03:18:55] WARNING: not removing hydrogen atom without neighbors -.[03:18:55] WARNING: no name column found on line 1 -[03:18:55] WARNING: no name column found on line 2 -[03:18:55] WARNING: no name column found on line 3 -[03:18:55] WARNING: no name column found on line 4 -[03:18:55] WARNING: no name column found on line 5 -[03:18:55] WARNING: no name column found on line 6 -[03:18:55] WARNING: no name column found on line 7 -[03:18:55] WARNING: no name column found on line 8 -[03:18:55] WARNING: no name column found on line 9 -[03:18:55] WARNING: no name column found on line 10 -[03:18:55] WARNING: no name column found on line 11 -[03:18:55] WARNING: no name column found on line 12 -[03:18:55] WARNING: no name column found on line 13 -[03:18:55] WARNING: no name column found on line 14 -[03:18:55] WARNING: no name column found on line 15 -[03:18:55] WARNING: no name column found on line 16 -[03:18:55] WARNING: no name column found on line 17 -[03:18:55] WARNING: no name column found on line 18 -[03:18:55] WARNING: no name column found on line 19 -[03:18:55] WARNING: no name column found on line 20 -[03:18:55] WARNING: no name column found on line 21 -[03:18:55] WARNING: no name column found on line 22 -[03:18:55] WARNING: no name column found on line 23 -[03:18:55] WARNING: no name column found on line 24 -[03:18:55] WARNING: no name column found on line 25 -[03:18:55] WARNING: no name column found on line 26 -[03:18:55] WARNING: no name column found on line 27 -[03:18:55] WARNING: no name column found on line 28 -[03:18:55] WARNING: no name column found on line 29 -[03:18:55] WARNING: no name column found on line 30 -[03:18:55] WARNING: no name column found on line 31 -[03:18:55] WARNING: no name column found on line 32 -[03:18:55] WARNING: no name column found on line 33 -[03:18:55] WARNING: no name column found on line 34 -[03:18:55] WARNING: no name column found on line 35 -[03:18:55] WARNING: no name column found on line 36 -[03:18:55] WARNING: no name column found on line 37 -[03:18:55] WARNING: no name column found on line 38 -[03:18:55] WARNING: no name column found on line 39 -[03:18:55] WARNING: no name column found on line 40 -[03:18:55] WARNING: no name column found on line 41 -[03:18:55] WARNING: no name column found on line 42 -[03:18:55] WARNING: no name column found on line 43 -[03:18:55] WARNING: no name column found on line 44 -[03:18:55] WARNING: no name column found on line 45 -[03:18:55] WARNING: no name column found on line 46 -[03:18:55] WARNING: no name column found on line 47 -[03:18:55] WARNING: no name column found on line 48 -[03:18:55] WARNING: no name column found on line 49 -[03:18:55] WARNING: no name column found on line 50 -[03:18:55] WARNING: no name column found on line 51 -[03:18:55] WARNING: no name column found on line 52 -[03:18:55] WARNING: no name column found on line 53 -[03:18:55] WARNING: no name column found on line 54 -[03:18:55] WARNING: no name column found on line 55 -[03:18:55] WARNING: no name column found on line 56 -[03:18:55] WARNING: no name column found on line 57 -[03:18:55] WARNING: no name column found on line 58 -[03:18:55] WARNING: no name column found on line 59 -[03:18:55] WARNING: no name column found on line 60 -[03:18:55] WARNING: no name column found on line 61 -[03:18:55] WARNING: no name column found on line 62 -[03:18:55] WARNING: no name column found on line 63 -[03:18:55] WARNING: no name column found on line 64 -[03:18:55] WARNING: no name column found on line 65 -[03:18:55] WARNING: no name column found on line 66 -[03:18:55] WARNING: no name column found on line 67 -[03:18:55] WARNING: no name column found on line 68 -[03:18:55] WARNING: no name column found on line 69 -[03:18:55] WARNING: no name column found on line 70 -[03:18:55] WARNING: no name column found on line 71 -[03:18:55] WARNING: no name column found on line 72 -[03:18:55] WARNING: no name column found on line 73 -[03:18:55] WARNING: no name column found on line 74 -[03:18:55] WARNING: no name column found on line 75 -[03:18:55] WARNING: no name column found on line 76 -[03:18:55] WARNING: no name column found on line 77 -[03:18:55] WARNING: no name column found on line 78 -[03:18:55] WARNING: no name column found on line 79 -[03:18:55] WARNING: no name column found on line 80 -[03:18:55] WARNING: no name column found on line 81 -[03:18:55] WARNING: no name column found on line 82 -[03:18:55] WARNING: no name column found on line 83 -[03:18:55] WARNING: no name column found on line 84 -[03:18:55] WARNING: no name column found on line 85 -[03:18:55] WARNING: no name column found on line 86 -[03:18:55] WARNING: no name column found on line 87 -[03:18:55] WARNING: no name column found on line 88 -[03:18:55] WARNING: no name column found on line 89 -[03:18:55] WARNING: no name column found on line 90 -[03:18:55] WARNING: no name column found on line 91 -[03:18:55] WARNING: no name column found on line 92 -[03:18:55] WARNING: no name column found on line 93 -[03:18:55] WARNING: no name column found on line 94 -[03:18:55] WARNING: no name column found on line 95 -[03:18:55] WARNING: no name column found on line 96 -[03:18:55] WARNING: no name column found on line 97 -[03:18:55] WARNING: no name column found on line 98 -[03:18:55] WARNING: no name column found on line 99 -[03:18:55] WARNING: no name column found on line 100 -[03:18:55] WARNING: no name column found on line 101 -[03:18:55] WARNING: no name column found on line 102 -[03:18:55] WARNING: no name column found on line 103 -[03:18:55] WARNING: no name column found on line 104 -[03:18:55] WARNING: no name column found on line 105 -[03:18:55] WARNING: no name column found on line 106 -[03:18:55] WARNING: no name column found on line 107 -[03:18:55] WARNING: no name column found on line 108 -[03:18:55] WARNING: no name column found on line 109 -[03:18:55] WARNING: no name column found on line 110 -[03:18:55] WARNING: no name column found on line 111 -[03:18:55] WARNING: no name column found on line 112 -[03:18:55] WARNING: no name column found on line 113 -[03:18:55] WARNING: no name column found on line 114 -[03:18:55] WARNING: no name column found on line 115 -[03:18:55] WARNING: no name column found on line 116 -[03:18:55] WARNING: no name column found on line 117 -[03:18:55] WARNING: no name column found on line 118 -[03:18:55] WARNING: no name column found on line 119 -[03:18:55] WARNING: no name column found on line 120 -[03:18:55] WARNING: no name column found on line 121 -[03:18:55] WARNING: no name column found on line 122 -[03:18:55] WARNING: no name column found on line 123 -[03:18:55] WARNING: no name column found on line 124 -[03:18:55] WARNING: no name column found on line 125 -[03:18:55] WARNING: no name column found on line 126 -[03:18:55] WARNING: no name column found on line 127 -[03:18:55] WARNING: no name column found on line 128 -[03:18:55] WARNING: no name column found on line 129 -[03:18:55] WARNING: no name column found on line 130 -[03:18:55] WARNING: no name column found on line 131 -[03:18:55] WARNING: no name column found on line 132 -[03:18:55] WARNING: no name column found on line 133 -[03:18:55] WARNING: no name column found on line 134 -[03:18:55] WARNING: no name column found on line 135 -[03:18:55] WARNING: no name column found on line 136 -[03:18:55] WARNING: no name column found on line 137 -[03:18:55] WARNING: no name column found on line 138 -[03:18:55] WARNING: no name column found on line 139 -[03:18:55] WARNING: no name column found on line 140 -[03:18:55] WARNING: no name column found on line 141 -[03:18:55] WARNING: no name column found on line 142 -[03:18:55] WARNING: no name column found on line 143 -[03:18:55] WARNING: no name column found on line 144 -[03:18:55] WARNING: no name column found on line 145 -[03:18:55] WARNING: no name column found on line 146 -[03:18:55] WARNING: no name column found on line 147 -[03:18:55] WARNING: no name column found on line 148 -[03:18:55] WARNING: no name column found on line 149 -[03:18:55] WARNING: no name column found on line 150 -[03:18:55] WARNING: no name column found on line 151 -[03:18:55] WARNING: no name column found on line 152 -[03:18:55] WARNING: no name column found on line 153 -[03:18:55] WARNING: no name column found on line 154 -[03:18:55] WARNING: no name column found on line 155 -[03:18:55] WARNING: no name column found on line 156 -[03:18:55] WARNING: no name column found on line 157 -[03:18:55] WARNING: no name column found on line 158 -[03:18:55] WARNING: no name column found on line 159 -[03:18:55] WARNING: no name column found on line 160 -[03:18:55] WARNING: no name column found on line 161 -[03:18:55] WARNING: no name column found on line 162 -[03:18:55] WARNING: no name column found on line 163 -[03:18:55] WARNING: no name column found on line 164 -[03:18:55] WARNING: no name column found on line 165 -[03:18:55] WARNING: no name column found on line 166 -[03:18:55] WARNING: no name column found on line 167 -[03:18:55] WARNING: no name column found on line 168 -[03:18:55] WARNING: no name column found on line 169 -[03:18:55] WARNING: no name column found on line 170 -[03:18:55] WARNING: no name column found on line 171 -[03:18:55] WARNING: no name column found on line 172 -[03:18:55] WARNING: no name column found on line 173 -[03:18:55] WARNING: no name column found on line 174 -[03:18:55] WARNING: no name column found on line 175 -[03:18:55] WARNING: no name column found on line 176 -[03:18:55] WARNING: no name column found on line 177 -[03:18:55] WARNING: no name column found on line 178 -[03:18:55] WARNING: no name column found on line 179 -[03:18:55] WARNING: no name column found on line 180 -[03:18:55] WARNING: no name column found on line 181 -[03:18:55] WARNING: no name column found on line 182 -[03:18:55] WARNING: no name column found on line 183 -[03:18:55] WARNING: no name column found on line 184 -[03:18:55] WARNING: no name column found on line 185 -[03:18:55] WARNING: no name column found on line 186 -[03:18:55] WARNING: no name column found on line 187 -[03:18:55] WARNING: no name column found on line 188 -[03:18:55] WARNING: no name column found on line 189 -[03:18:55] WARNING: no name column found on line 190 -[03:18:55] WARNING: no name column found on line 191 -[03:18:55] WARNING: no name column found on line 192 -[03:18:55] WARNING: no name column found on line 193 -[03:18:55] WARNING: no name column found on line 194 -[03:18:55] WARNING: no name column found on line 195 -[03:18:55] WARNING: no name column found on line 196 -[03:18:55] WARNING: no name column found on line 197 -[03:18:55] WARNING: no name column found on line 198 -[03:18:55] WARNING: no name column found on line 199 -[03:18:55] WARNING: no name column found on line 200 -[03:18:55] WARNING: no name column found on line 201 -[03:18:55] WARNING: no name column found on line 202 -[03:18:55] WARNING: no name column found on line 203 -[03:18:55] WARNING: no name column found on line 204 -[03:18:55] WARNING: no name column found on line 205 -[03:18:55] WARNING: no name column found on line 206 -[03:18:55] WARNING: no name column found on line 207 -[03:18:55] WARNING: no name column found on line 208 -[03:18:55] WARNING: no name column found on line 209 -[03:18:55] WARNING: no name column found on line 210 -[03:18:55] WARNING: no name column found on line 211 -[03:18:55] WARNING: no name column found on line 212 -[03:18:55] WARNING: no name column found on line 213 -[03:18:55] WARNING: no name column found on line 214 -[03:18:55] WARNING: no name column found on line 215 -[03:18:55] WARNING: no name column found on line 216 +..[12:29:16] WARNING: not removing hydrogen atom without neighbors +.[12:29:16] WARNING: not removing hydrogen atom without neighbors +.[12:29:16] WARNING: no name column found on line 1 +[12:29:16] WARNING: no name column found on line 2 +[12:29:16] WARNING: no name column found on line 3 +[12:29:16] WARNING: no name column found on line 4 +[12:29:16] WARNING: no name column found on line 5 +[12:29:16] WARNING: no name column found on line 6 +[12:29:16] WARNING: no name column found on line 7 +[12:29:16] WARNING: no name column found on line 8 +[12:29:16] WARNING: no name column found on line 9 +[12:29:16] WARNING: no name column found on line 10 +[12:29:16] WARNING: no name column found on line 11 +[12:29:16] WARNING: no name column found on line 12 +[12:29:16] WARNING: no name column found on line 13 +[12:29:16] WARNING: no name column found on line 14 +[12:29:16] WARNING: no name column found on line 15 +[12:29:16] WARNING: no name column found on line 16 +[12:29:16] WARNING: no name column found on line 17 +[12:29:16] WARNING: no name column found on line 18 +[12:29:16] WARNING: no name column found on line 19 +[12:29:16] WARNING: no name column found on line 20 +[12:29:16] WARNING: no name column found on line 21 +[12:29:16] WARNING: no name column found on line 22 +[12:29:16] WARNING: no name column found on line 23 +[12:29:16] WARNING: no name column found on line 24 +[12:29:16] WARNING: no name column found on line 25 +[12:29:16] WARNING: no name column found on line 26 +[12:29:16] WARNING: no name column found on line 27 +[12:29:16] WARNING: no name column found on line 28 +[12:29:16] WARNING: no name column found on line 29 +[12:29:16] WARNING: no name column found on line 30 +[12:29:16] WARNING: no name column found on line 31 +[12:29:16] WARNING: no name column found on line 32 +[12:29:16] WARNING: no name column found on line 33 +[12:29:16] WARNING: no name column found on line 34 +[12:29:16] WARNING: no name column found on line 35 +[12:29:16] WARNING: no name column found on line 36 +[12:29:16] WARNING: no name column found on line 37 +[12:29:16] WARNING: no name column found on line 38 +[12:29:16] WARNING: no name column found on line 39 +[12:29:16] WARNING: no name column found on line 40 +[12:29:16] WARNING: no name column found on line 41 +[12:29:16] WARNING: no name column found on line 42 +[12:29:16] WARNING: no name column found on line 43 +[12:29:16] WARNING: no name column found on line 44 +[12:29:16] WARNING: no name column found on line 45 +[12:29:16] WARNING: no name column found on line 46 +[12:29:16] WARNING: no name column found on line 47 +[12:29:16] WARNING: no name column found on line 48 +[12:29:16] WARNING: no name column found on line 49 +[12:29:16] WARNING: no name column found on line 50 +[12:29:16] WARNING: no name column found on line 51 +[12:29:16] WARNING: no name column found on line 52 +[12:29:16] WARNING: no name column found on line 53 +[12:29:16] WARNING: no name column found on line 54 +[12:29:16] WARNING: no name column found on line 55 +[12:29:16] WARNING: no name column found on line 56 +[12:29:16] WARNING: no name column found on line 57 +[12:29:16] WARNING: no name column found on line 58 +[12:29:16] WARNING: no name column found on line 59 +[12:29:16] WARNING: no name column found on line 60 +[12:29:16] WARNING: no name column found on line 61 +[12:29:16] WARNING: no name column found on line 62 +[12:29:16] WARNING: no name column found on line 63 +[12:29:16] WARNING: no name column found on line 64 +[12:29:16] WARNING: no name column found on line 65 +[12:29:16] WARNING: no name column found on line 66 +[12:29:16] WARNING: no name column found on line 67 +[12:29:16] WARNING: no name column found on line 68 +[12:29:16] WARNING: no name column found on line 69 +[12:29:16] WARNING: no name column found on line 70 +[12:29:16] WARNING: no name column found on line 71 +[12:29:16] WARNING: no name column found on line 72 +[12:29:16] WARNING: no name column found on line 73 +[12:29:16] WARNING: no name column found on line 74 +[12:29:16] WARNING: no name column found on line 75 +[12:29:16] WARNING: no name column found on line 76 +[12:29:16] WARNING: no name column found on line 77 +[12:29:16] WARNING: no name column found on line 78 +[12:29:16] WARNING: no name column found on line 79 +[12:29:16] WARNING: no name column found on line 80 +[12:29:16] WARNING: no name column found on line 81 +[12:29:16] WARNING: no name column found on line 82 +[12:29:16] WARNING: no name column found on line 83 +[12:29:16] WARNING: no name column found on line 84 +[12:29:16] WARNING: no name column found on line 85 +[12:29:16] WARNING: no name column found on line 86 +[12:29:16] WARNING: no name column found on line 87 +[12:29:16] WARNING: no name column found on line 88 +[12:29:16] WARNING: no name column found on line 89 +[12:29:16] WARNING: no name column found on line 90 +[12:29:16] WARNING: no name column found on line 91 +[12:29:16] WARNING: no name column found on line 92 +[12:29:16] WARNING: no name column found on line 93 +[12:29:16] WARNING: no name column found on line 94 +[12:29:16] WARNING: no name column found on line 95 +[12:29:16] WARNING: no name column found on line 96 +[12:29:16] WARNING: no name column found on line 97 +[12:29:16] WARNING: no name column found on line 98 +[12:29:16] WARNING: no name column found on line 99 +[12:29:16] WARNING: no name column found on line 100 +[12:29:16] WARNING: no name column found on line 101 +[12:29:16] WARNING: no name column found on line 102 +[12:29:16] WARNING: no name column found on line 103 +[12:29:16] WARNING: no name column found on line 104 +[12:29:16] WARNING: no name column found on line 105 +[12:29:16] WARNING: no name column found on line 106 +[12:29:16] WARNING: no name column found on line 107 +[12:29:16] WARNING: no name column found on line 108 +[12:29:16] WARNING: no name column found on line 109 +[12:29:16] WARNING: no name column found on line 110 +[12:29:16] WARNING: no name column found on line 111 +[12:29:16] WARNING: no name column found on line 112 +[12:29:16] WARNING: no name column found on line 113 +[12:29:16] WARNING: no name column found on line 114 +[12:29:16] WARNING: no name column found on line 115 +[12:29:16] WARNING: no name column found on line 116 +[12:29:16] WARNING: no name column found on line 117 +[12:29:16] WARNING: no name column found on line 118 +[12:29:16] WARNING: no name column found on line 119 +[12:29:16] WARNING: no name column found on line 120 +[12:29:16] WARNING: no name column found on line 121 +[12:29:16] WARNING: no name column found on line 122 +[12:29:16] WARNING: no name column found on line 123 +[12:29:16] WARNING: no name column found on line 124 +[12:29:16] WARNING: no name column found on line 125 +[12:29:16] WARNING: no name column found on line 126 +[12:29:16] WARNING: no name column found on line 127 +[12:29:16] WARNING: no name column found on line 128 +[12:29:16] WARNING: no name column found on line 129 +[12:29:16] WARNING: no name column found on line 130 +[12:29:16] WARNING: no name column found on line 131 +[12:29:16] WARNING: no name column found on line 132 +[12:29:16] WARNING: no name column found on line 133 +[12:29:16] WARNING: no name column found on line 134 +[12:29:16] WARNING: no name column found on line 135 +[12:29:16] WARNING: no name column found on line 136 +[12:29:16] WARNING: no name column found on line 137 +[12:29:16] WARNING: no name column found on line 138 +[12:29:16] WARNING: no name column found on line 139 +[12:29:16] WARNING: no name column found on line 140 +[12:29:16] WARNING: no name column found on line 141 +[12:29:16] WARNING: no name column found on line 142 +[12:29:16] WARNING: no name column found on line 143 +[12:29:16] WARNING: no name column found on line 144 +[12:29:16] WARNING: no name column found on line 145 +[12:29:16] WARNING: no name column found on line 146 +[12:29:16] WARNING: no name column found on line 147 +[12:29:16] WARNING: no name column found on line 148 +[12:29:16] WARNING: no name column found on line 149 +[12:29:16] WARNING: no name column found on line 150 +[12:29:16] WARNING: no name column found on line 151 +[12:29:16] WARNING: no name column found on line 152 +[12:29:16] WARNING: no name column found on line 153 +[12:29:16] WARNING: no name column found on line 154 +[12:29:16] WARNING: no name column found on line 155 +[12:29:16] WARNING: no name column found on line 156 +[12:29:16] WARNING: no name column found on line 157 +[12:29:16] WARNING: no name column found on line 158 +[12:29:16] WARNING: no name column found on line 159 +[12:29:16] WARNING: no name column found on line 160 +[12:29:16] WARNING: no name column found on line 161 +[12:29:16] WARNING: no name column found on line 162 +[12:29:16] WARNING: no name column found on line 163 +[12:29:16] WARNING: no name column found on line 164 +[12:29:16] WARNING: no name column found on line 165 +[12:29:16] WARNING: no name column found on line 166 +[12:29:16] WARNING: no name column found on line 167 +[12:29:16] WARNING: no name column found on line 168 +[12:29:16] WARNING: no name column found on line 169 +[12:29:16] WARNING: no name column found on line 170 +[12:29:16] WARNING: no name column found on line 171 +[12:29:16] WARNING: no name column found on line 172 +[12:29:16] WARNING: no name column found on line 173 +[12:29:16] WARNING: no name column found on line 174 +[12:29:16] WARNING: no name column found on line 175 +[12:29:16] WARNING: no name column found on line 176 +[12:29:16] WARNING: no name column found on line 177 +[12:29:16] WARNING: no name column found on line 178 +[12:29:16] WARNING: no name column found on line 179 +[12:29:16] WARNING: no name column found on line 180 +[12:29:16] WARNING: no name column found on line 181 +[12:29:16] WARNING: no name column found on line 182 +[12:29:16] WARNING: no name column found on line 183 +[12:29:16] WARNING: no name column found on line 184 +[12:29:16] WARNING: no name column found on line 185 +[12:29:16] WARNING: no name column found on line 186 +[12:29:16] WARNING: no name column found on line 187 +[12:29:16] WARNING: no name column found on line 188 +[12:29:16] WARNING: no name column found on line 189 +[12:29:16] WARNING: no name column found on line 190 +[12:29:16] WARNING: no name column found on line 191 +[12:29:16] WARNING: no name column found on line 192 +[12:29:16] WARNING: no name column found on line 193 +[12:29:16] WARNING: no name column found on line 194 +[12:29:16] WARNING: no name column found on line 195 +[12:29:16] WARNING: no name column found on line 196 +[12:29:16] WARNING: no name column found on line 197 +[12:29:16] WARNING: no name column found on line 198 +[12:29:16] WARNING: no name column found on line 199 +[12:29:16] WARNING: no name column found on line 200 +[12:29:16] WARNING: no name column found on line 201 +[12:29:16] WARNING: no name column found on line 202 +[12:29:16] WARNING: no name column found on line 203 +[12:29:16] WARNING: no name column found on line 204 +[12:29:16] WARNING: no name column found on line 205 +[12:29:16] WARNING: no name column found on line 206 +[12:29:16] WARNING: no name column found on line 207 +[12:29:16] WARNING: no name column found on line 208 +[12:29:16] WARNING: no name column found on line 209 +[12:29:16] WARNING: no name column found on line 210 +[12:29:16] WARNING: no name column found on line 211 +[12:29:16] WARNING: no name column found on line 212 +[12:29:16] WARNING: no name column found on line 213 +[12:29:16] WARNING: no name column found on line 214 +[12:29:16] WARNING: no name column found on line 215 +[12:29:16] WARNING: no name column found on line 216 ...... ---------------------------------------------------------------------- -Ran 10 tests in 0.083s +Ran 10 tests in 0.174s OK .................. ---------------------------------------------------------------------- -Ran 18 tests in 0.526s +Ran 18 tests in 1.335s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.057s +Ran 3 tests in 0.177s OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.020s +Ran 8 tests in 0.062s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.014s +Ran 2 tests in 0.056s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.010s +Ran 2 tests in 0.039s OK . ---------------------------------------------------------------------- -Ran 1 test in 0.047s +Ran 1 test in 0.164s OK ........ @@ -27470,7 +27497,7 @@ OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.003s +Ran 3 tests in 0.012s OK ... @@ -27480,27 +27507,27 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.002s +Ran 4 tests in 0.015s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.009s +Ran 7 tests in 0.025s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.011s +Ran 4 tests in 0.048s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 1.509s +Ran 4 tests in 6.230s OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.031s +Ran 10 tests in 0.123s OK . @@ -27510,23 +27537,23 @@ OK .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.004s +Ran 10 tests in 0.014s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.046s +Ran 5 tests in 0.090s OK -.........[03:19:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -[03:19:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -[03:19:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -[03:19:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -.......[03:19:08] Molecule does not have explicit Hs. Consider calling AddHs() -[03:19:08] Molecule does not have explicit Hs. Consider calling AddHs() +.........[12:29:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +[12:29:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +[12:29:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +[12:29:56] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +.......[12:29:56] Molecule does not have explicit Hs. Consider calling AddHs() +[12:29:56] Molecule does not have explicit Hs. Consider calling AddHs() ..... ---------------------------------------------------------------------- -Ran 21 tests in 3.224s +Ran 21 tests in 12.096s OK mol_197 @@ -27540,7 +27567,7 @@ Ran 1 test in 0.000s OK -...[03:19:08] +...[12:29:58] **** Pre-condition Violation @@ -27551,63 +27578,63 @@ . ---------------------------------------------------------------------- -Ran 4 tests in 0.013s +Ran 4 tests in 0.038s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 4.193s +Ran 2 tests in 12.761s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.054s +Ran 2 tests in 0.120s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.008s +Ran 3 tests in 0.012s OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.013s +Ran 4 tests in 0.030s OK -.....[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors -[03:19:15] WARNING: not removing hydrogen atom without neighbors +.....[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors +[12:30:16] WARNING: not removing hydrogen atom without neighbors ..... ---------------------------------------------------------------------- -Ran 10 tests in 0.189s +Ran 10 tests in 0.710s OK ssssss..........s/build/reproducible-path/rdkit-202309.3/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 22 tests in 2.864s +Ran 22 tests in 12.141s OK (skipped=7) sss. ---------------------------------------------------------------------- -Ran 4 tests in 0.261s +Ran 4 tests in 0.982s OK (skipped=3) ssss @@ -27617,42 +27644,46 @@ OK (skipped=4) .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.489s +Ran 10 tests in 2.225s OK -...[03:19:21] SMARTS Parse Error: syntax error while parsing: boromicacid -[03:19:21] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' -[03:19:21] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide -[03:19:21] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' -[03:19:21] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride -[03:19:21] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' -[03:19:21] reaction has no reactants -[03:19:21] reaction has no products -[03:19:21] initialization failed -[03:19:21] reaction has no reactants -[03:19:21] reaction has no products +...[12:30:41] SMARTS Parse Error: syntax error while parsing: boromicacid +[12:30:41] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid' +[12:30:41] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide +[12:30:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide' +[12:30:41] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride +[12:30:41] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride' +[12:30:41] reaction has no reactants +[12:30:41] reaction has no products +[12:30:41] initialization failed +[12:30:41] reaction has no reactants +[12:30:41] reaction has no products . ---------------------------------------------------------------------- -Ran 4 tests in 0.022s +Ran 4 tests in 0.136s OK ['C[C@@H](F)CN', 'C[C@@H](F)CN |a:1|', 'C[C@H](F)CN |o1:1|', 'C[C@H](F)CN |&1:1|'] .... ---------------------------------------------------------------------- -Ran 4 tests in 0.007s +Ran 4 tests in 0.032s OK ........................ ---------------------------------------------------------------------- -Ran 24 tests in 0.050s +Ran 24 tests in 0.246s OK !!! TEST FAILURE: python UnitTestDescriptors.py {} +5: [12:37:23] Finished: testMultipleTimes() +5: [12:37:23] +5: ----------------------------------------- +222/222 Test #5: testConcurrentQueue .................... Passed 751.37 sec 99% tests passed, 2 tests failed out of 222 -Total Test time (real) = 113.67 sec +Total Test time (real) = 751.47 sec The following tests FAILED: 20 - testConrec (Failed) @@ -30379,28 +30410,28 @@ dh_shlibdeps -a -O--buildsystem=cmake dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package postgresql-16-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: 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: package postgresql-16-rdkit: 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: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined +dpkg-gencontrol: warning: package postgresql-16-rdkit: 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: package librdkit1t64: 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-16-rdkit: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202309.3-4~exp1_all.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202309.3-4~exp1_arm64.deb'. -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-4~exp1_arm64.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202309.3-4~exp1_all.deb'. dpkg-deb: building package 'postgresql-16-rdkit' in '../postgresql-16-rdkit_202309.3-4~exp1_arm64.deb'. -dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202309.3-4~exp1_arm64.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-4~exp1_arm64.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202309.3-4~exp1_arm64.deb'. +dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202309.3-4~exp1_all.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-4~exp1_arm64.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202309.3-4~exp1_all.deb'. +dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202309.3-4~exp1_arm64.deb'. dpkg-deb: building package 'postgresql-16-rdkit-dbgsym' in '../postgresql-16-rdkit-dbgsym_202309.3-4~exp1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202309.3-4~exp1_arm64.buildinfo dpkg-genchanges --build=binary -O../rdkit_202309.3-4~exp1_arm64.changes @@ -30409,12 +30440,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2570913/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2570913/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/3420888 and its subdirectories -I: Current time: Fri May 10 03:21:58 -12 2024 -I: pbuilder-time-stamp: 1715354518 +I: removing directory /srv/workspace/pbuilder/2570913 and its subdirectories +I: Current time: Fri Jun 13 12:41:01 +14 2025 +I: pbuilder-time-stamp: 1749768061